Returning crop residues to the field after harvesting is a proven effective strategy for improving soil fertility, carbon sequestration, and crop productivity. However, the relationships between crop residue return modes, SOC and nutrient contents, and crop yields are still unclear. In this study, a field trial was conducted to investigate the effects of different maize straw return modes, i.e., straw mulching (SMU), straw deep ploughing (SDP), and control without straw return (CK), on soil organic carbon (SOC) and nutrient contents in soil layers of 0–40 cm in a Mollisol. The relationships between straw return modes, SOC and nutrient contents, and maize yield were evaluated. Compared with CK, SMU and SDP significantly increased SOC, total nitrogen (N), available N, total phosphorus (P), and available P contents in all soil layers. Relative to SMU, SOC, total N, available N, total P, and available P contents were significantly lower in soil layers of 0–10 cm, but they were significantly higher in soil layers of 20–40 cm in SDP. Redundancy analysis indicated that total N, available N, and SOC were major factors controlling maize yield. Structural equation modeling further showed that straw return modes indirectly affected maize yield by directly and preferentially affecting total N and available N contents. The results indicated that SMU and SDP were beneficial for increasing SOC and nutrient contents at the surface and subsurface soils, respectively. Optimizing a nitrogen management strategy is important to achieve high maize yield with straw return.