With rapid urbanization, increasing amounts of chemicals are being used in our daily life. Emerging organic contaminants are a large class of chemicals that are widely detected in the environment. They include pharmaceuticals and personal care products, pesticides, perfluorinated compounds, and endocrine-disrupting compounds. Recently, many countries have reported the occurrence of emerging organic contaminants. In addition, emerging organic contaminants are frequently detected in various environmental samples, including river and lake water samples. Despite their low concentrations in the environment, emerging organic contaminants are potential risks to humans and wildlife. Because they could lead to endocrine disrupting effects and the occurrence of resistance genes. Thus, the detection of emerging organic contaminants in the environment is imperative for ecological systems and human health. The recent development of analytical techniques has led to the identification of more emerging organic contaminants in the environment. At present, the commonly used chromatographic separation techniques include liquid chromatography and gas chromatography. For the identification and quantitation of emerging organic contaminants, chromatography is usually combined with spectroscopy or mass spectrometry. The concentrations of emerging organic contaminants are not sufficiently high to be detected directly, and the matrix is complex in environmental samples. Emerging organic contaminants also have diverse properties. Thus, environmental samples must be pretreated before detection. Pretreatment includes the concentration and purification of the environmental samples. The commonly used pretreatment methods are ultrasound-assisted extraction, QuEChERS, liquid-liquid extraction, and solid-phase extraction. With the development of pretreatment methods, solid-phase microextraction and stirred-bar adsorption extraction have also become popular. These sample pretreatment methods have many advantages such as good efficiency and effectivity for recycling target compounds. Hence, they are widely used. However, these methods are time-consuming, in addition to requiring expensive consumables and large amounts of organic solvents. Lyophilization is a technique used for product dehydration, preservation, and storage in the agricultural and food industries. It is also occasionally used to simplify the extraction procedure for drug residue analysis. There are three stages of lyophilization: freezing, primary drying, and secondary drying. Lyophilization has many advantages when used for pretreatment, namely, operational simplicity, less consumables, less sample volume, prolonged storage, and minimal sample loss. Lyophilization is thus an alternative method for the pretreatment of emerging organic contaminants in environmental samples. Recently, lyophilization has been applied to the pretreatment of emerging organic contaminants in environmental water samples. In general, a few steps were included during sample analysis. First, the samples were pretreated and frozen before the primary drying stage. After lyophilization, the analytes were extracted using a small amount of organic solvent and dried with nitrogen. Consequently, the elution was reconstructed and detected after dryness and filtration. Many groups of emerging organic contaminants could be recovered, including antibiotics, pesticides, and endocrine-disrupting compounds. The lyophilization could be automated, so that minimal manual intervention was required. By adopting lyophilization, good recoveries and accuracies were achieved. A few cleanup processes were conducted, and a small amount of organic solvent was consumed. Thus, lyophilization is a highly prospective pretreatment method for monitoring emerging organic contaminants, and can be extended to a diverse range of these contaminants. For large-scale and high-frequency sampling campaigns, cheap and convenient pretreatment is urgently needed. In this study, typical emerging organic contaminants are described, along with the universal types of such contaminants and the principles of lyophilization. The application of lyophilization to the detection of emerging organic contaminants in the environment is also introduced. The future of lyophilization is discussed, which provides a reference for emerging contaminant detection in environmental samples.