This study investigates the utility of plant δ¹3C natural labeling in predicting the impacts of environmental shifts on carbon cycling within ecosystems, particularly focusing on paddy fields treated with maize (Zea mays L.) residues and biochar. Specifically, it examines how soil δ¹3C and the sources of soil organic carbon (SOC), respond in paddy fields (which cultivate C3 plants like rice) when amended with maize residues, maize biochar, and silica-enriched biochar (derived from C4 plants). Conducted in the Fuzhou paddy fields, the experiment included control groups and treatment groups with maize residue (4 t ha⁻¹), maize biochar (4 t ha⁻¹), and silicon-modified maize biochar (4 t ha⁻¹) during both the early and late rice growth periods. The results indicate that all soil treatments increased soil δ¹3C. The application of maize residues notably affected the δ¹3C of the upper soil profile (0–15 cm) differently from the deeper layers (15–30 cm), and it increased soil organic C more than biochar or silicon-modified maize biochar. Soil available P (AP) and pH emerged as significant factors linking δ¹3C, influencing rice yield through changes in soil physicochemical properties. Unlike maize residues, which reduced rice yields, applications of biochar and silicon-modified maize biochar increased rice yields. The latter, which was particularly effective in lowering SOC decomposition rates and addressing rice's silica needs, emerged as the preferred option. The study highlights maize biochar and silicon-modified maize biochar as sustainable alternatives to maize residues for rice cultivation, enhancing soil fertility, carbon pool stability, and yields.