Bemisia tabaci is an important pest affecting agricultural and horticultural crops worldwide and comprises a complex of cryptic species. In China, the introduction of the two invasive cryptic species, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), has considerably affected the ecological niche of the native cryptic species. Based on occurrence records obtained through field surveys and high-resolution environmental data, using maximum entropy modelling, we established ecological niche models to predict the distribution of invasive and native cryptic species of B. tabaci in China and identified the differences in ecological niches. The results showed that the distribution range and niche breadth of the invasive cryptic species exceed that of the native cryptic species in the order of MED > MEAM1 > China1 > Asia1. There are different degrees of niche overlap and range overlap between cryptic species. Moreover, the important environmental variables affecting their distribution were different, as well as their response and adaptation to most environmental variables. Our results suggest that the B. tabaci species complex occupies a complex ecological niche in China. The findings improve our understanding of the ecological characteristics of B. tabaci species complex, which will be useful in the development of prevention and control strategies for this pest in China.