In older, unlogged rainforest of Hainan Island, China, leaves of saplings were larger, and fine root systems of saplings were thicker with fewer root tips than in historically logged areas. These results were consistent among 15 Angiosperm lineages, even though families differed widely in their leaf and root traits. How plant organ morphologies vary with environment is key for inferring plant functional strategies. We were interested in quantifying any changes in fine root and leaf morphology of saplings with local-scale environmental variation in tropical forest, and if any variation in organ morphologies differed with plant lineage. We measured functional traits of fine root systems and leaves of saplings from 15 families in historically logged and unlogged Chinese tropical forest, where soil fertility and texture slightly decreased with greater forest age. Root morphological traits were more conservative, while leaf morphologies were more acquisitive in primary forest than in secondary forest. From secondary to primary forests, mean root system diameter increased 0.4 mm, mean specific root length decreased 3.5 m kg−1, and mean root system branching intensity decreased by 0.3 tips cm−1. Similarly, from secondary to primary forests, average leaf area increased 7 cm2 and specific leaf area decreased 0.8 m2 kg−1. Leaf thickness and root tissue density were not different. Among the selected plant families, root and leaf morphological differences between forest types were consistent. Within lineage (i.e., intraspecific) root and leaf morphological variation showed contrasting patterns. Local-scale variation in soil phosphorus and base saturation affected intraspecific variation in root diameter and specific root length.