Small waterbodies are a unique aquatic ecosystem with an increasing recognition for their important role in maintaining regional biodiversity and delivering ecosystem services. However, small waterbodies in Northwest Yunnan, one of the most concerned global biodiversity hot-spots, remain largely unknown. Here, we investigated the community structure of crustacean zooplankton and their relationships with limnological, morphometric and spatial variables in the highland small waterbodies in Northwest Yunnan in both the dry (October 2015) and rainy (June 2016) seasons. A total of 38 species of crustacean zooplankton were identified in our study, which is significantly higher than many other reported waterbodies in the Yunnan-Guizhou plateau as well as in the Yangtze River basin. This suggests that the highland small waterbodies are critical in maintaining regional zooplankton diversity in Northwest Yunnan. Meanwhile, we found limnological variables could explain most variation of crustacean zooplankton community, comparing to the morphometric and spatial variables in both the rainy and dry seasons. Our study revealed the diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan and highlighted the importance of small waterbodies in maintaining regional biodiversity.