In recent years, the frequency of extreme climate events in subtropical regions has increased, and changes in the frequency and interval of heat waves have made the patterns of heat waves and their stress on plants more diverse. High frequency heat waves not only affected the carbon sequestration rate of plants through heat stress, but also hindered the hydraulic structure of plants through water stress, affecting the transportation of carbohydrates. However, the response of subtropical tree hydraulic structures and non-structural carbohydrates (NSCs) to complex heat wave patterns is still unclear. This study conducted a heat wave simulation experiment on the seedlings of the main subtropical broad-leaved tree species Phoebe bournei and Schima superba, focusing on the effects of different heat wave frequencies (once or twice) and different interval times between multiple heat waves (short interval, medium interval, and long interval) on the hydraulic structure characteristics and NSCs of the stems of the seedlings. The hydraulic conductivity (K_h), maximum hydraulic conductivity (K_max), specific hydraulic conductivity (K_s), percentage loss of hydraulic conductivity (PLC) in the hydraulic structure were measured using a flushing method, and the content of non-structural carbohydrates in the stems was determined using an anthrone sulfuric acid colorimetric method. The results showed that (1) there were significant differences in the hydraulic structure and non-structural carbohydrates between Phoebe bournei and Schima superba in tree species. (2) The frequency of heat waves had significant impact on the K_max and PLC of Phoebe bournei and Schima superba. (3) The interval between repeated heatwaves became longer, and the embolism of Schima superba stems decreased, while the embolism of Phoebe bournei stems increased. The more severe the embolism, the less NSC content in the stems. Overall, the water conductivity of the stem of Phoebe bournei seedlings was relatively fragile, with severe embolism and decrease in water conductivity after heat waves, and NSC had little effect in alleviating embolism function. However, Schima superba had strong water conductivity. If sufficient recovery time is obtained after a heat wave, its water conductivity can be fully restored, and its recovery degree is closely related to NSC content. The results of this study indicate that the occurrence of high frequency heat waves significantly affects the hydraulic conductivity of the stems of Phoebe bournei and Schima superba seedlings, and there are differences in the effects of repeated heat wave intervals on the hydraulic structure of plants. Additionally, there are differences in the tolerance and tolerance mechanisms of the two subtropical broad-leaved tree species to high temperature and water stress associated with heat waves.