The study on dynamics of crop yields, sustainable yield index (SYI) and agronomic efficiency of fertilizer under different fertilization systems including the treatment of N, NP, NK, PK, NPK, NPK+M (manure), NPK+S (crop straw) and CK (no fertilizer) were carried out based on 14 years’ long term fertilizer experiment in Drab Fluvo-aquic soil in Beijing. The results showed that N and P were two crucial limited nutrients of crop yield in Drab Fluvo-aquic Soil. In NPK treatment yield of wheat was increased by 459%, 386%, 280%, 205%, and corn by 154%, 108%, 87%, 78%, respectively, compared with these in CK, N, NK, PK treatments. The yield of NPK+M treatment was more 12% than that of NPK treatment. However, the yield of NPK+S was similar to that of the NPK treatment. The sustainable yield indexes of NPK, NPK+M and NPK+S treatments were greater than those of other treatments. The output of yields per unit fertilizer (i.e. agronomic efficiency of fertilizer, AEF) was varied considerably with different crops and combinations of fertilizers applied. The AEF of N for wheat and corn by single use of N fertilizer was reduced, while that of NPK treatment was 16 kg/kg N for wheat and 14 kg/kg N for corn and had an increase tendency during the experiment period. The AEF of P in wheat was greater than that in corn, further more, the AEF of P was 4.5–7.0 times higher than that at the beginning of the experiment 10 years ago. The AEF of K was negative in NK treatment, while increased rapidly in NPK treatment after 10-year crop cultivation; K was also one of critical limited nutrients for crop yield. The AEF of farmyard manure (FYM) in NPK +M treatment was 21 kg/t of wheat and 25 kg/t for corn, while the AEF of crop straw in NPK+S treatment was negative for wheat and 37 kg/t for corn. Soil O.M, total N, P and available N, P, K content were increased in NPK treatment. The accumulations of soil O.M and N, P, K nutrients were accelerated in NPK+M and NPK+S treatments. On the contrary, total N, total P were exhausted in the treatments without N, P fertilizer. Available P, K had the same variation trend in the treatments without P, K fertilizer.