In arid and semi-arid ecosystems, the duration of vegetation response to rainfall pulses varies with the magnitude and timing of the precipitation event. Extreme weather events, such as tropical cyclones, can trigger long-lasting ecological responses. In this study, we examined the impact of tropical cyclones on ecosystem gross primary production (GPP) in the Pilbara, Western Australia, and identified two distinct effects: direct and legacy effects. Our findings reveal that tropical cyclones delivering substantial rainfall lead to an immediate increase in GPP. This direct effect typically persists for approximately two months. Following this initial GPP increase, the ecosystems exhibit altered responses to subsequent rainfalls, a phenomenon we define as the legacy effect, which lasts for about 100 days. On average, tropical cyclones contribute an additional 30 g C/m2/y GPP during a water year, with 40% of this additional GPP attributed to the legacy effect, compared with tropical-cyclone-unaffected areas in the semi-arid tropics of Western Australia. However, prolonged drought can diminish the legacy effect. These findings improve our understanding of how changes in precipitation patterns driven by global climate change may influence carbon assimilation and ecosystem resilience in semi-arid regions.