The functional balance between leaves and roots is believed to be mediated by the specific location of shoots and roots, i.e. differences in transport distances and degrees of organ connectivity. However, it remains unknown whether the adaptive responses of trees to biomass removal depend on the relative orientation of leaf and root pruning. Here, we applied five pruning treatments to saplings of Cunninghamia lanceolata (Chinese fir) under field and glasshouse conditions, namely no pruning (control), half of lateral branches pruned, half of lateral roots pruned, half of the branches and roots pruned on the same side of the plant, and half of the branches and roots pruned on opposite sides of the plant. The effects of pruning on the growth, carbon storage and allocation, and physiology of leaves and fine roots on the same and opposite sides of the plant were investigated. Compared with the effect of root-pruning on leaves, fine roots were more limited by carbon availability and their physiological activity was more strongly reduced by shoot pruning, especially when branches on the same side of the plant were removed. Pruning of branches and roots on the opposite side of the plant resulted in the lowest carbon assimilation rates and growth among all treatments. The results of a stable-isotope labeling indicated that less C was distributed to fine roots from the leaves on the opposite side of the plant compared to those on the same side, but N allocation from roots to leaves depended less on the relative root and leaf orientation. The results collectively indicate that the functional responses of C. lanceolata to pruning are not only determined by the source-sink balance model but are also related to interactions between leaves and fine roots. We argue that the connectivity among lateral branches and roots depends on their relative orientation, which is therefore critical for the functional balance between leaves and fine roots.