Sugarcane/soybean intercropping and reduced nitrogen (N) application as an important sustainable agricultural pattern can increase crop primary productivity and improve soil ecological functions, thereby affecting soil organic carbon (SOC) input and turnover. To explore the potential mechanism of sugarcane/soybean intercropping affecting SOC sequestration, a two-factor long-term field experiment was carried out, which included planting pattern (sugarcane monocropping (MS), sugarcane/soybean 1:1 intercropping (SB1), and sugarcane/soybean 1:2 intercropping (SB2)) and nitrogen addition levels (reduced N application (N1: 300 kg·hm-2) and conventional N application (N2: 525 kg·hm-2)). The results showed that the shoot and root C fixation in the sugarcane/soybean intercropping system were significantly higher than those in the sugarcane monocropping system during the whole growth period of sugarcane, and the N application level had no significant effect on the C fixation of plants in the intercropping system. Sugarcane/soybean intercropping also increased the contents of total organic C (TOC), labile organic C fraction [microbial biomass C (MBC) and dissolved organic C (DOC)] in the soil during the growth period of sugarcane, and this effect was more obvious at the N1 level. We further analyzed the relationship between plant C sequestration and SOC fraction content using regression equations and found that both plant shoot and root C sequestration were significantly correlated with TOC, MBC, and DOC content. This suggests that sugarcane/soybean intercropping increases the amount of C input to the soil by improving crop shoot and root C sequestration, which then promotes the content of each SOC fraction. The results of this study indicate that sugarcane/soybean intercropping and reduced N application patterns can synergistically improve plant and soil C fixation, which is of great significance for improving crop yields, increasing soil fertility, and reducing greenhouse gas emissions from agricultural fields.