Tillage systems can changes in soil organic carbon dynamics and soil microbial biomass by changing aggregate formation and C distribution within the aggregate. Wheat straw ditch-buried returning (WD) had significantly higher total organic carbon than did wheat straw returning with ploughing (WP) and no straw returning (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 wheat straw returning with rotary tillage (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. The content of SOC in WSA_ma increased on average in the following order: T < G < G+NPK₁ < G+NPK₃ < T+FYM. Intensive soil cultivation in the T treatment resulted in a statistically significant build-up of SOC in WSA_ma at an average rate of 1.33, 1.18, 0.97, 1.22 and 0.76 g/kg/y across the size fractions > 5 mm, 5‒3 mm, 2‒1 mm, 1‒0.5 mm and 0.5‒0.25 mm, respectively. The content of non-labile carbon reflected the contents of SOC in WSA. The highest labile carbon (C_L) in WSA_ma, as compared to others, was found in T+FYM. Overall, application of higher NPK doses resulted in higher content of C_L in WSA_ma compared with the lower applications of NPK. On the other hand, lower applications of NPK to soil increased the content of CL in WSA_mi, as compared to G+NPK₃.However, higher SOC content of 8.14 gkg^-1of soil was found in reduced tilled residue retained plots followed by 10.34 g kg^-1in furrow irrigated raised beds with residue retained plots. Whereas, the lowest level of SOC content of 5.49 gkg^-1of soil were found in puddled transplanted rice followed by wheat planted under conventionally tilled plots. Average SOC concentration of the control treatment was 0.54%, which increased to 0.65% in the RDF treatment and 0.82% in the RDF+FYM treatment. Compared to F₁control treatment the RDF+FYM treatment sequestered 0.33 Mg C ha^-1yr^-1 whereas the NPK treatment sequestered 0.16 Mg Cha^-1yr^-1. Long term conservation tillage significantly increased 66.1%, 57.9%, 50.9%,38.3%,37.3% and 32% LFOC, SOC, PON, TN, LFON, DOC and POC, over conventional tillage (T₇) treatment and WSC 39.6% in surface soil and 37.4% in subsurface soil. Under RWCS, TOC contents were similar in 50% RDN as CF+50% RDN as GM/SPM (F₆) and1/3^rdN as CF+1/3^rdN as FYM+1/3^rdN as GM/SPM (F₇) and 75% RDN as CF+25% RDN as FYM (F₃) plots and significantly higher than those in control (no manure and fertilizer) (F₁) plots (by 50.4% 48.3%, and 43.3% respectively).