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Fertilization is an effective technique to improve soil fertility and increase crop yield. The long-term effects of different fertilizers on soil considerably vary. Over 38 consecutive years of different fertilization positioning experiments in a double cropping rice field of Qiyang Red Soil Experimental Station, seven different fertilization treatments including CK (no fertilization), NPK (nitrogen, phosphorus, and potassium fertilizer), M (cow manure), NPKM (nitrogen, phosphorus, and potassium with cow manure), NPM (nitrogen and phosphorus with cow manure), NKM (nitrogen and potassium with cow manure), and PKM (phosphorus and potassium with cow manure) were applied to study the effects on rice yield, soil fertility, and nutrient apparent balance in a paddy field. The results showed that the annual average yields of rice in NPKM, NPM, NKM, PKM, M, NPK and CK treatments ranged from 6 214 to 11 562 kg ha–1. Yields under long-term organic and inorganic treatments (NPKM, NPM, NKM and PKM) were 22.58, 15.35, 10.53 and 4.41%, respectively, greater than under the NPK treatment. Soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN) and available potassium (AK) concentration with long-term organic and inorganic treatment (NPKM, NPM, NKM and PKM) were significantly higher than in inorganic fertilizer (NPK) treatments. Soil total phosphorus (TP) and available phosphorus (AP) contentration with organic fertilizer combined with inorganic N and P fertilizer treatment (NPKM, NPM and PKM) were significantly higher than with inorganic fertilizer alone (NPK treatments). The average annual rice yield (11 562 kg ha–1), SOC (20.88 g kg–1), TN (2.30 g kg–1), TP (0.95 g kg–1), TK (22.50 g kg–1) and AP (38.94 mg kg–1) concentrations were the highest in the NPKM treatment. The soil AN concentration (152.40 mg kg–1) and AK contentration (151.00 mg kg–1) were the highest in the NKM treatment. N and P application led to a surplus of nitrogen and phosphorus in the soil, but NPKM treatment effectively reduced the surplus compared with other treatments. Soils under all treatments were deficient in potassium. Correlation analysis showed that SOC, TN, AN, TP, and AP contentration was significantly correlated with rice yield; the correlation coefficients were 0.428, 0.496, 0.518, 0.501, and 0.438, respectively. This study showed that the combined application of N, P, and K with cow manure had important effects on rice yield and soil fertility, but balanced application of N, P, and K with cow manure was required.