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Excessive fertilizer input, low nutrient use efficiency, soil quality, and environmental degradation hinder greenhouse vegetable production. Integrated agronomic strategies of soil, crop, and nutrient management are needed to sharply improve the vegetable yield and simultaneously maintain sustainable production. A three-season field experiment was conducted from 2015 to 2018, aiming to evaluate the effect of integrated soil–crop system management (ISSM) on the agronomy, environment, and economy of greenhouse vegetable systems in the Yangtze River Basin, China. Three treatments were included in the experiment: (1) farmers' current practice (FP), based on a local farmers' survey; (2) soil remediation treatment (SR), the application of soil conditioner and compost fertilizer instead of chicken manure; (3) ISSM, a combination of soil conditioner, reducing plant density, and using formula fertilizer as well as increasing the fertilization times. The results indicated that ISSM (47.7 Mg ha−1) improved the pepper yield by 17% relative to farmers' current practice (FP, 40.7 Mg ha−1). Soil remediation (SR), as a single approach, mainly made a contribution to improving the yield (by 6.9%) and nutrient use efficiency while reducing apparent nitrogen (N) losses. Higher yields were mainly attributed to increasing the fruit number per plant. On average, apparent N losses were reduced by 245 kg N ha−1 per season for ISSM compared to FP. In addition, higher net profits were obtained under SR and ISSM relative to FP. Overall, both SR and ISSM have advantages for the agronomy, environment, and economy in greenhouse vegetable production, but ISSM would be the optimal choice to achieve higher yields with lower environmental impacts. [ABSTRACT FROM AUTHOR]