This paper describes the effects of chemical fertiliser and pig manure application on the phosphorus (P) balance and changes of soil organic P (Po) fractions in a Mollisol following 14 years of maize–soybean–wheat rotation in Northeast China. The experiment was designed according to the local crop rotation and management system, consisting of a control treatment with no fertiliser application, a treatment with chemical nitrogen (N) and P fertilisers, and a treatment with chemical N and P fertilisers plus pig manure. The results suggest that the levels of local chemical fertiliser applications seem to balance the P removal by the crops, while the additional P in the pig manure resulted in substantial accumulation of P in the soil despite greater crop production. Analysis of Po fractions showed that long-term cultivation without fertilisation reduced the soil labile Po. Additions of P through application of chemical fertilisers only preserved the labile Po content, whereas addition of chemical P fertiliser plus pig manure increased the labile Po content. Comparison between 1993 and 2007 soil samples indicates that the moderately labile Po content declined in all treatments, whereas the non-labile Po content increased. These results suggest that the moderately labile Po may be transformed into labile Po and Pi, and that some active P fractions were immobilised during long-term cultivation. Adding fertiliser increased P availability and alleviated soil P immobilisation.