Pines have heteroblastic foliage (primary and secondary needles) during seedling stage, but how heteroblastic foliage affects carbon storage and biomass accumulation, contributing to seedling quality, is unclear. We investigated the influences of heteroblastic foliage on photosynthetic physiological characteristics, non-structural carbohydrate (NSC) and biomass accumulation in current-year seedlings; the key factors determining biomass accumulation were mainly determined by principal component screening, Spearman correlation, and path analysis. The results indicated that (1) primary needles have high photosynthetic pigments (chlorophyll a and total chlorophyll), net photosynthetic rates (Pn), the potential maximum photochemical efficiency (Fv/Fm), and leaf instantaneous water use efficiency (WUEi), whereas higher non-photochemical quenching (NPQ) suggested that sudden light increases induce the initiation of quenching mechanism in primary needles; additionally, secondary needles had a lower transpiration rate (Tr), limiting stomata (Ls), and light saturation point. (2) Secondary needles promoted soluble sugar (fructose and glucose) increases in leaves compared to that of primary needles and increased the leaf biomass accumulation (from 47.06% to 54.30%), enhancing the overall ability of photosynthetic organs; additionally, secondary needles can enhance the proportion of starch storage in the roots, and NSC accumulation was significantly increasing in the seedling leaves and roots. (3) Photosynthetic pigments (carotenoids, chlorophyll a, and total chlorophyll) had direct positive effects on primary needle seedling (PNS) biomass and promoted biomass by indirectly increasing soluble sugar synthesis in the stems. The Pn was the main physiological factor determining PNS biomass accumulation. In addition, the WUEi, Ls, and NPQ had direct negative effects on PNS biomass accumulation, inhibiting photosynthesis to limit seedling growth. Considering the functional traits in heteroblastic foliage is necessary when assessing different leaf types of Pinus massoniana (Lamb.) seedlings, in particular those threats implicated in light, water, and temperature relations. Our results can be beneficial to guide the establishment of seedling management and afforestation measures.