Straw ditch-buried returning is a new straw returning mode; however, the different effect of straw ditch-buried returning and frequently used straw returning modes on soil organic carbon (SOC) sequestration is still unclear. A 2 yr field experiment was conducted and four treatments (CK: no straw returning; WR: wheat straw returning with rotary tillage; WP: wheat straw returning with plowing; WD: wheat straw ditch-buried returning) were set to assess the effects on SOC fractions and sequestration in rice–wheat rotation. Results indicated that WD had significantly higher total organic carbon than did WP and CK in wheat season. Soil dissolved organic carbon and easily oxidizable carbon contents were significantly increased by 21.3%, 24.3%, 38.6%, and 43.5% under WR than that under CK in rice and wheat seasons, respectively. Soil microbial biomass carbon (MBC) content was highest under WP in rice season, but in wheat season, WR had significantly higher MBC than WP and WD. Soil carbon pool management index was significantly higher in WR than CK, with the increase of 41.0% and 108.6%. After 2 yr rotation, WD had a significant higher SOC stock and sequestration than WP. Therefore, WD could be an available mode to increase SOC sequestration in rice–wheat rotation system.