With a cropping area of 7.0 million hm2, the black soil (Typic hapludoll) region of Northeast China plays a crucial role in food security to the regional and whole country. In fact, the application of chemical fertilizer is an effective and fast way to increase crop production in a relatively short time. Recently, organic manure application has almost disappeared because its application in cropping system is both labor-demanding and uneconomical. However, there is limited information on crop yields under long-term fertilization of organic and inorganic fertilizers in this rotation system. Nutrient input/output and balance in farmland is critical for nutrient management, scientific distribution and application of fertilizer resources, and improving nutrient use efficiency, etc. The study was conducted to reveal the difference of grain yield and nutrient balance based on the average crop yields, the variation trends of crop yields and apparent balance of soil nutrients under different long-term fertilization conditions in black soil, and to provide scientific references for establishing effective long-term fertilization mode and promoting the sustainable development of crop production. A long-term experiment with various fertilizations was carried out during 1979-2014 in a rotation system with wheat (Triticum Aestivium L.)-soybean (Glycine max Merr.)-maize (Zea mays L.) in black soil area of Northeast China. The experiment consisted of 5 treatments: non-fertilization (CK), conventional chemical fertilizer (wheat: N 150kg/hm2, P2O5 75 kg/hm2, soybean: N 75kg/hm2, P2O5 150 kg/hm2, corn: N 150kg/hm2, P2O5 75 kg/hm2, K2O 75kg/hm2, NPK), conventional horse manure (18 600 kg/hm2 , M), conventional horse manure plus chemical fertilizer(the amount of chemical fertilizer was same as NPK, and the amount of horse manure was same as M), and 200% of the MNP (horse manure and chemical fertilizer, the amount was 2 times that of MNP, M2N2P2,). The results showed that: 1) Compared with the treatment CK, long-term application of chemical fertilizers (NPK) or long-term application of chemical fertilizers combined with horse manure (MNPK, M2N2P2) increased average crop yield (from 1980 to 2014) by 82.5%-91.6% (wheat) and 35.6%-40.9% (maize), respectively. In respect of average crop yield of 35 years, the treatments displayed an order of M2N2P2 >MNPK > NPK >M, but no significant differences were observed between M2N2P2, MNPK and NPK. 2) The yields of wheat and maize in CK decreased by 13.93 and 42.61 kg/(hm2·a) respectively, while the yield of soybean in CK increased by 7.409 kg/(hm2·a) with the experiment going. It showed the yield trend of wheat, soybean and maize in the treatment with fertilization overall increased with the experiment going. 3) Under the conditions of our experiment, surplus of nitrogen and phosphorus appeared in soil in the treatments of NPK and MNPK, and the increasing amounts were 29.7 and 17.5 kg/hm2 for nitrogen, and 33.4 and 61.2 kg/hm2 for phosphorus, respectively. Potassium deficit of 30.4-73.0 kg/hm2 was observed in all treatments. Compared with NPK, the supplement of nitrogen and potassium could be improved by the combined application of organic manure and inorganic fertilizer (MNPK) by 12.2 and 27.6 kg/hm2, respectively. 4) Crop yield was significantly positively correlated with the contents of organic matter, available nitrogen, available phosphorus, accumulated precipitation and daily mean temperature in the growth period (P<0.05). 5) Based on the characteristics of nutrient balance, we proposed the method of fertilizer application, i.e. keeping application amount of nitrogen stable, reducing phosphorus amount and increasing potassium amount under rotation system of wheat, soybean and corn in black soil area.