Abstract: Owing to global climate change and human activity, abiotic and biotic stresses occur frequently, threatening crop yield and food safety. Reducing the effects of biotic and abiotic stresses is crucial for improving agricultural productivity. Silicon fertilizers are ecologically compatible and environmentally friendly. Silicon has been proven to alleviate plant stress under various conditions, indicating considerable application prospects. Systematic examination of the mitigation mechanisms of silicon on various abiotic and biotic stresses can provide guidance for future practice and research. In this review, we first introduced the absorption and deposition of silicon within plant organs, and the effect of silicon on the synthesis and metabolism of carbon-based substances (“Silicon-Carbon Trade-off Hypothesis”), and then summarized the eco-physiological alleviation mechanisms of abiotic stresses including osmotic stress, nutrient deficiency stress, heavy metal stress, extreme temperature, ultraviolet stress, and biotic stress. We concluded that the common mechanisms of silicon to improve plant stress resistance included improvement of anti-oxidation activities, enhancement of photosynthetic ability, and carbon-silicon trade-off; however, the mechanisms differed under different stresses. Furthermore, previous studies had mainly focused on the eco-physiological mechanisms of the effects of silicon, particularly on grass families such as rice, and the effects of silicon on carbon cycling in agricultural ecosystems had been largely ignored. Therefore, this paper concluded with an outlook on further studies on the molecular mechanisms of silicon, modifications of legume-rhizobia relationships, and significance of phytolith carbon sequestration in agricultural ecosystems. We aimed to provide help and references for broader and deeper investigations of silicon.