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Due to their inherent advantages, silica nanoparticles (SiNPs) have greatly potential applications as bioactive materials in biosensors/biomedicine. However, the long-term and nonspecific accumulation in healthy tissues may give rise to toxicity, thereby impeding their widespread clinical application. Hence, it is imperative and noteworthy to develop biodegradable and clearable SiNPs for biomedical purposes. Recently, the design of multi-stimuli responsive SiNPs to improve degradation efficiency under specific pathological conditions has increased their clinical trial potential as theranostic nanoplatform. This review comprehensively summaries the rational design and recent progress of biodegradable SiNPs under various internal and external stimuli for rapid in vivo degradation and clearance. In addition, the factors that affect the biodegradation of SiNPs are also discussed. We believe that this systematic review will offer profound stimulus and timely guide for further research in the field of SiNP-based nanosensors/nanomedicine. In this review, we will comprehensively discuss the rational design of stimuli-responsive biodegradable SiNPs based on doping strategy in native structures. The latest biological application of biodegradable SiNPs that incorporate endogenous and exogenous stimuli are aslo thoroughly summarized. We finally tried to provide the encountered challenges that need to be solved on the way of SiNPs to the clinic. We comprehensively discuss stimuli-responsive silica nanoparticles from native structure designs, summarize the biological applications of biodegradable SiNPs, and provide the challenges that need to be solved in the future. [Display omitted] • We comprehensively discussed stimuli-responsive biodegradable SiNPs based on doping strategy in native structures. • The latest biological application of biodegradable SiNPs that incorporate endogenous and exogenous stimuli were summarized. • We finally tried to provide the encountered challenges that need to be solved on the way of SiNPs to the clinic. [ABSTRACT FROM AUTHOR]