By using a pot experiment under natural rainfall, nitrogen (N) and phosphorus (P) leaching, nutrient accumulation, and crop yield under peanut-radish rotation in two red clay soils of different fertilities (high and low) which received pig manure at gradient dosages combined with zero, halved or conventional rates of chemical fertilizers were monitored, and thereby safe pig manure digestion capacities of the two red soils were estimated. The results showed that nutrient leaching was dominated by nitrate N and no risk was for P leaching. Nitrate N concentration in leachate peaked about one month after seed sowing and fertilization, increasing with the increase of pig manure application rate, and afterwards declined rapidly below the limit of Class III groundwater quality standard of China. In the peak time, nitrate N concentration in leachate was significantly higher in the high-fertility red soil than in the low-fertility one, and the risk of exceeding nitrate N limit was high for the high-fertility red soil under the conditions of high rates of pig manure in combination with chemical fertilizers. The application of pig manure easily led to bioavailable P accumulation in soil, more pronounced in the high-fertility soil, but no significant accumulation for inorganic N in both soils. Peanut yield of the low-fertility red soil increased with the increasing of pig manure application rate, while that of the high-fertility one leveled off over a certain rate of pig manure. Considering all the effects of pig manuring on groundwater (leaching), soil and crop production, it is estimated that the low– and high–fertility red clay soils have safe pig manure digestion capacities of P 400 and 100 kg/(hm2·a), respectively (equivalent to wet composted pig manure of 91.2 and 22.8 t/(hm2·a), respectively) under the condition of no chemical fertilizers, and P 400 and 25 kg/(hm2·a), respectively (equivalent to wet composted pig manure of 91.2 and 5.7 t/(hm2·a), respectively) under the condition of halved chemical fertilizers. It is advised that pig manure be applied in large part to low–fertility red clay soils in southern regions of China.