Top pruning is an effective way to produce "orchard-style" forest seed orchards, and phosphorus (P) fertilization can improve the reproductive ability of Masson pine (Pinus massoniana) to some extent. However, it is necessary to determine the absorption and distribution of carbon (C) and nitrogen (N) nutrients by applying phosphorus fertilizer under top pruning. Two clones, high-yielding (209) and low-yielding (225), were tested in a pot experiment with 15N markers during early floral primordium. Calcium magnesium phosphate fertilizer was applied at doses of 0 g/plant (P0), 200 g/plant (P2), and 400 g/plant (P4) to the test plots without top pruning (N-TP) and with top pruning (TP). Overall, top pruning promoted female cone formation in high-yielding P. massoniana clones and significantly affected the downward movement of the fruiting layer, the density of female cones in the lower branches increased by 25.45%~64.97% after top pruning. However, their impact on the formation of female cones in low-yield clones was limited. Top pruning altered the variation of C:N, N:P ratios by increasing C, N and P contents of lower branches. Compared with no top pruning, the C:N ratios of lower branches of 209 and 225 clones increased by 5.79%~27.38% and 2.57%~13.60% after top pruning, respectively. At flowering period, the distribution ratios of N and P in high-yielding female cones increased by 175.0% and 46.3% after top pruning, respectively, indicating that top pruning promoted the absorption of N and P content to female cones. The interaction effect between top pruning and P fertilizer had a significant impact on female cone density, The application of P fertilizer can improve the N harvesting ability of P. massoniana under top-pruning measures, especially by increasing the C:N ratio in the second layer of coniferous branches in the lower part of the tree and promoting the distribution of N to female flower heads, which is beneficial for improving seed yield. On the whole, top pruning causes changes in the spatial structure of trees, affecting the redistribution of nutrients and promoting the distribution of N and P to female cones; The application of phosphorus fertilizer not only regulates the carbon to nitrogen ratio of needles, but also improves the N and P nutrient absorption capacity of P. massoniana under the combination of top pruning measures, which helps to distribute nutrients to organs related to the formation of female cones. The study confirmed that top pruning and phosphorus fertilization increased the probability of high yield and altered the nutrient distribution characteristics in P. massoniana.