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Japanese larch (Larix kaempferi = L. leptolepis) is often characterized by its high growth rate with heterophyllous shoots, but the functional differences of heterophyllous shoots still remain unclear. Recently, abrupt high temperature and drought during spring induced high photosynthetic rate via change in leaf morphology of the deciduous habit. In order to reveal the photosynthetic characteristics of both short and long-shoot needles of sunny canopy of the larch trees using a canopy tower, we calculated the seasonal change of gas exchange characters and leaf mass per area (LMA) and foliar nitrogen content (N) of heterophyllous needles: short and long-shoot needles over 3 years. No marked difference in light-saturated photosynthetic rates (Psat) was observed between short and long shoots after leaf maturation to yellowing, although the difference was obvious in a specific year, which only shows that seasonal change in temperature and soil moisture determines the in situ photosynthetic capacity of needles. The large annual and seasonal variations in Psat in both shoots were found to be mainly determined by climatic variations, while shoot types determined the strategy of their photosynthetic N utilization as well as the stomatal regulation.