Open AccessTo explore the effects of different fertilization regimes on soil organic matter (SOM) sequestration in a winter-soybean/corn rotation, a long-term field experiment was conducted in Anhui, China, from 1982 to 2011. There were six treatments, as follows: (1) no fertilizer input (CK); (2) mineral fertilizers input (NPK); (3) mineral fertilizers + 3,750 kg ha-1 wheat straw (WS/2-NPK); (4) mineral fertilizers + 7,500 kg ha-1 wheat straw (WS-NPK); (5) mineral fertilizers + 15,000 kg ha-1 composted farmyard manure (CNPK); and (6) mineral fertilizers + 30,000 kg ha-1 composted farmyard manure (DNPK). Mineral fertilizer applications combined with organic amendments improved soil physical properties. For the WS/2-NPK, WS-NPK, CNPK and DNPK treatments, the soil bulk density decreased more than 10%, while the air porosity and field water content increased more than 90% and 15%, compared with the values at the start of the experiment in 1982. Our results indicate that about two decades are needed for SOM to reach its saturation point in all treatments. The SOM sequestration rate was related to the fertilization regime. The average SOM sequestration rate in 1982-2005 was 0.27 g kg-1 yr-1 with NPK, 0.45 g kg-1 yr-1 with WS/2-NPK, 0.56 g kg-1 yr-1 with WS-NPK, 0.60 g kg-1 yr-1 with CNPK and 1.02 g kg-1 yr-1 with DNPK. Therefore, both the quantity and the quality of the organic amendment determine the SOM sequestration rate and SOM saturation level.