Pinus massoniana is the pioneer tree species in the red soil regions of southern China, however, its growth is impaired by the poor soil fertility. This study examined the effects of compound fertilizer, microbial fertilizer and super absorbent polymer (SAP) on the growth characteristics, biomass, plant nutrient content, and fertilizer uptake efficiency (FUE) of 1-year-old Pinus massoniana seedlings. A control (no fertilizer, CK) and three fertilization treatments, namely single application of compound fertilizer (0.94, 1.89, 3.56 g); mixed application of compound fertilizer and microbial fertilizer ((0.94+8.00), (1.89+8.00), (3.56+8.00) g); and mixed application of compound fertilizer and SAP ((0.94+1.01), (1.89+1.01), (3.56+1.01) g), were applied over 2 years. The results showed that: (1) Compared to the control, different fertilization treatments significantly increased the ground diameter and plant height growth of seedlings. The highest growth of seedling ground diameter and plant height were both F2B (mixed application of compound fertilizer and SAP, (1.89 + 1.01) g) treatments, which was significantly higher than other treatments. (2) Under the mixed application of compound fertilizer and microbial fertilizer, root biomass accounted for a larger proportion of the whole biomass. Meanwhile, under the mixed application of compound fertilizer and SAP, the whole biomass of the seedlings was higher. (3) Fertilization significantly increased the TN, TP, TK contents of leaves, stems, and roots of the seedlings. The TP content of seedlings had the greatest impact on its growth characteristics and is extremely significantly correlated, which explains 58.03% of the changes in seedling growth characteristics (P < 0.01). (4) Principal component analysis indicated that the F2B ((1.89+1.01) g) was the optimum fertilization amount and method in this experiment. Comprehensive analysis of growth characteristics and FUE of the seedlings showed that the F2B ((1.89+1.01) g) might serve as a highly effective fertilization method for Pinus massoniana growing in the severely eroded and degraded red soils of southern China. These results provide a theoretical basis for the fertilization management of Pinus massoniana forests with severely eroded and degraded red soils.