Organic matter application significantly influences soil carbon storage and sequestration in cropland. The investigation of C sequestration through soil organic carbon (SOC) fractions in the soil profile and its relation to nutrient stoichiometry are essential for evaluating the effect of farming practice on soil fertility. This study aimed to examine the effect of cattle manure application on nutrient stoichiometry, which would be associated with soil C stock in SOC fractions, such as microbial biomass C (MBC), dissolved organic C (DOC) and water-soluble organic C (WSOC), coarse particulate organic carbon (cPOC), fine particulate organic carbon (fPOC) and the mineral-associated organic carbon (MOC). A four-year manure application experiment was conducted in a Mollisol, in which fertilization treatments comprised (1) NoF: the non-fertilizer control, (2) F: synthetic fertilizer, i.e. 20.3, 21.2 and 12.2 kg ha(-1) of nitrogen (N), phosphorus (P) and potassium (K) in soybean, and 69.0, 28.1 and 6.1 kg ha(-1) of N, P and K for corn on an annual basis, respectively, (3) F + M: synthetic fertilizer plus 15 Mg ha(-1) of cattle manure and (4) F + 2M: synthetic fertilizer plus 30 Mg ha(-1) of cattle manure in a soybean-corn rotation. SOC concentration in top 10 cm of soil was 18 % and 19 % higher under F + M than that under NoF and F, respectively. Whereas, F+2 M significantly increased SOC concentration by 32 %, 32 %, 14 %, and 11 % in 0-10, 10-20, 20-30, and 30-40 cm of soil depth compared to that in respective soil depth under NoF. Compared to NoF and F, manure application (F + M and F+2 M) significantly increased MBC in the top 30 cm of soil depth and DOC concentration in the top 20 cm of soil depth, but significantly decreased WSOC concentration in the top 20 cm of soil depth. F+2 M significantly increased cPOC concentration in the top 30 cm of soil depth compared to NoF and F. F + M significantly increased fPOC concentration in the top 50 cm of soil depth, compared to NoF, and F. F+2 M further increased the fPOC concentration in the top 30 cm of soil depth, compared to F + M. There was no difference among fertilization treatments in MOC concentration in any soil depth. There were significant exponential correlations of C concentration in POC fractions with soil N, P and N/P ratio. These results indicate that the combination of manure and synthetic fertilizer increased C accumulation in the POC fraction especially in the top 30 cm of soil depth. The change of nutrient stoichiometry was responsible to the accumulation of soil organic matter, highlighting that N, rather than P mainly regulated C accumulation in POC. Increasing input of N fertilizer combined with manure application would benefit the formation of soil organic matter in agricultural Mollisols.