Tillage practices affect soil organic carbon (SOC) pools, which in turn influence soil ecosystem processes. In this study we measured the effects of long-term conventional tillage (CT) and no-till (NT) practices on SOC and its fraction over the winter wheat growing season in surface and subsurface soils. Soil samples were taken during five physiological stages of winter wheat growth to a depth of 60 cm from the long-term (19 yr) experimental station on Loess Plateau in China. While the SOC content increased slowly in the surface soils during winter wheat growth with the NT treatment, it showed less fluctuation with the CT treatment. On average, NT treatment resulted in 82 and 53% higher SOC content in depth of 0 to 5 and 5 to 10 cm than CT treatment (P < 0.05). However, seasonal variations in microbial biomass carbon (MBC) and particulate organic carbon (POC) were similar under NT and CT, and showed maximum values in before-winter anthesis stage. The dissolved organic carbon (DOC) trend was highest before sowing, decreased before the winter and jointed stages, and increased again during the anthesis stage. Particulate organic carbon, MBC, and DOC were all significantly higher with NT than with CT in the upper 10 cm. Soil depth affected SOC and its fraction which decreased from surface to subsurface soil. The POC, MBC, and DOC were highly correlated with the SOC. This study demonstrated that measurements of the effect of tillage practices on SOC based on SOC fractions should include both seasonal changes and profile distribution.