Increasing soil organic carbon (SOC) stocks while maintaining high crop productivity remains a critical challenge in paddy-based cropping systems. Widely adopted conservation practices, such as no-till and straw mulching, often show limited potential for subsoil carbon sequestration and may even reduce yields under flooded conditions. Here, we evaluate a subsoil-oriented management practice, ditch-buried straw return (DB-SR), designed to address both constraints simultaneously. Based on a 15-year rice–wheat rotation field experiment, DB-SR significantly increased SOC stocks at 0–40 cm depth by 46%. DB-SR also increased grain yield by 15% without additional fertilizer inputs. Moreover, DB-SR reduced net CO₂-equivalent emissions by 34% and increased net economic benefits by 18%, indicating clear environmental and agronomic advantages. A meta-analysis of field studies across China further confirmed that DB-SR consistently outperformed other straw return and tillage practices in promoting subsoil SOC accumulation and increasing crop yield. Overall, our findings suggest that DB-SR shows strong potential as a subsoil management strategy to enhance subsoil carbon sequestration while sustaining high crop productivity.