Summer heatwaves have caused a distinct mortality between urban greening and native plants. However, there are insufficient studies revealing the underlying mechanisms. We hypothesized that differentiation in hydraulic traits and their integration cause the varied heatwave-induced damages between the two plant types. To prove it, three desert native species and five urban greening species were selected as the experimental objects. Then, the number of damaged individuals caused by summer heatwaves were investigated based on the 100 individuals for each species. The hydraulic traits (including hydraulic transport, photosynthetic and leaf traits) of 3–5 mature individuals were measured for each species. The comparative analysis (independent sample t test and one-way ANOVA) and the collaborative analysis (Pearson correlation and network analysis) were used to reveal the differences in heatwave-induced damage, hydraulic traits and their integration between urban greening and native plants. Our results showed that the heatwave-induced damage to urban greening plants was larger than that to native species. Water potentials of leaf and branch in pre-dawn and midday, P50, leaf dry matter content, net photosynthetic rate, transpiration rate and stomatal conductance of desert native species were significantly lower than those of urban greening plants (P < 0.05), while twig specific hydraulic conductivity, Huber value, wood density, intrinsic water use efficiency and the specific leaf area showed opposite patterns (P < 0.05). Trait integration of desert native species (0.63) was much higher than greening plants (0.24). Our results indicate that artificial urban greening plants are more susceptible to drought stress caused by heatwaves than native desert species. In the context of global climate change, in order to maintain the stability and function of urban ecosystems in extreme climate, the screening of greening plants should start from the perspective of hydraulics and trait integration, and more native species with strong drought adaptability should be planted.