Cunninghamia lanceolata seed orchard is the important guarantee for the cultivation of high and stable yield of Cunninghamia lanceolata varieties, and has positive significance in forestry production. Through the experimental research, this paper explored the abundance and deficiency of soil nutrients and the balance of nutrients in the third-generation seed orchard of Cunninghamia lanceolata and determined the optimal fertilizer ratio and fertilizer amount in the Cunninghamia lanceolata seed orchard to provide recommended fertilization formula in hilly red soil distribution area of northern Fujian. The fertilization experiment of N, P, K, Ca, Mg, B, Mo and other elements in the third-generation Cunninghamia lanceolata seed orchard in northern Fujian was carried out by using “3414” formula fertilization design. This study designed the fertilization levels of N, P and K (molybdenum fertilizer processing was added) and the fertilization levels of Ca, Mg and B respectively. And at the same time, it took the number (weight) of cones, seed ratio, seed yield and DBH as evaluation indexes and fitted the function equation of fertilizer effect to study the law of action among nutrients and proposed the optimal fertilizer ratio and fertilizer amount. The results showed that the nutrient contents of N, P, K, Ca and Mg in seed orchard soil were low, the content of B was in medium level, and the content of Mo was high; the combined effects of N, P, Mg and N-K, Ca-B fertilizers on the yield of seed orchard reached significant or extremely significant levels, while the effect of single fertilizer was smaller. And the effect of single application of K, Ca and B had almost no effect, while the effect of combined application of fertilizer was better. The comprehensive effect analysis results showed that the maximum yield fertilizer combination of seed orchard was: 100 g urea + 897 g superphosphate + 150 g potassium chloride + 150 g lime + 105 g magnesium sulfate + 75 g borax of per plant, and molybdenum fertilizer was applied to each plant. The dosage of N, P2O5, K2O, CaO, Mg, B and Mo was 46.0, 107.7, 90.0, 75.0, 31.4, 2.3 and 5.0 g, respectively, and the ratio was N: P2O5: K2O: CaO: Mg: B: Mo = 1.0:2.3:2.0:1.6:0.7:0.05:0.1. The multi-element formula fertilization could improve the yield and quality of Cunninghamia lanceolata seed orchard, the yield of single cone of per plant, single cone weight, seed ratio and seed orchard yield were significantly higher than those of the mother tree without fertilization. According to the fertilization scheme in this study, the seed orchard yield could reach 45.99-95.65 g/plant theoretically. The yield of the macroelement fertilization experiment reached 80% to 86% of the theoretical yield and the yield of the medium and trace element fertilization experiment was about 70% of the theoretical yield. The average yield of the actual seed orchard was about 40% of the predicted yield. It is expected that the yield of the third-generation seed orchard of Cunninghamia lanceolata could be greatly improved by rational fertilization.