The accumulation of phytolith-occluded organic carbon (PhytOC) in soil is a potential pathway for long-term organic carbon sequestration. Silicon fertilizer, an exogenous silicon amendment, can enhance carbon sequestration by phytoliths in crops, while biochar plays an active role in reducing soil greenhouse gas emissions. To investigate the pathways through which combined application of silicon fertilizer and biochar affected the carbon sequestration capacity of phytoliths and its impact on soil greenhouse gas emissions, four treatments were established, including control (CK), silicon fertilizer (SF), biochar (BC), and a mixed application of silicon fertilizer and biochar (BS). The distribution characteristics of soil silicon fractions were analyzed through field experiments combined with laboratory phytolith stability grading tests to confirm differences in PhytOC sequestration and its stability in different maize organs. Additionally, the effects of mixed exogenous silicon on crop agronomic characteristics and the reduction of soil greenhouse gas emissions were elucidated. The results indicated that under the BS treatment, the contents of readily soluble silicon (CaCl2-Si), unstable silicon on the surface of inorganic soil particles (Acetic-Si), and unstable silicon on the surface of soil organic matter (H2O2-Si), exhibited an initial increase followed by a decrease, while the content of weakly crystalline silicates and amorphous silicon (Na2CO3-Si) showed a continuous decline. BS treatment significantly increased the phytolith content of the maize stem, sheath, and leaf by 54.75%, 5.68%, and 56.87%, respectively, compared with CK. The crop PhytOC production flux reached 57.79kg/(hm2·a). The stable phytolith content was increased by 16.32 percentage points, and the stable PhytOC production flux reached 34.12kg/(hm2·a). Furthermore, the global warming potential (GWP) under combined application was 3716.88kg/hm2. The results demonstrated that combined application of silicon fertilizer and biochar significantly enhanced the carbon sequestration capacity of crop phytoliths and reduction of soil greenhouse gas emissions, providing strategies and methodologies for achieving long-term carbon sequestration.