Although dam removal has been considered a viable strategy to mitigate habitat fragmentation within a stream, long-term ecosystem effects after dam removal have rarely been discussed. In an effort to enhance the resilience of the critically endangered Formosan salmon (Oncorhynchus masou formosanus) in response to climate change, a 15-m-high check dam in a subtropical high-mountain stream was half-removed. The aim of this study was to analyze the long-term response of trophic structure and function to dam removal by constructing Ecopath models upstream and downstream of the removed dam at different times. Field surveys for model parameters were conducted for a complete seasonal cycle 1 year before dam removal, 1 and 2 years (short-term) after dam removal and 7 and 8 years (long-term) after dam removal. Both upstream and downstream systems moved toward maturity after dam removal. In the short term after dam removal, more energy can be transferred further up in the food webs. The vitality and diversity of both systems also increased. In the long term after dam removal, although the transfer efficiencies of both systems generally showed a decreasing pattern, the resilience increased. Compared to the upstream system, the effects of dam removal on the downstream system were more evident. In the downstream system, dam removal enhanced the vitality of the Formosan salmon and thus the top-down control. The dominance of detritivory flow in the food web also shifted toward the dominance of herbivory flow. Consequently, the downstream system reached more maturity, and the food web was more closely linked. The ecosystem attributes of the upstream and downstream systems converged, suggesting that the decoupling between upstream and downstream systems resulting from damming disappeared 8 years after dam removal.