The species complex of sweet potato whitefly, comprises at least 44 morphologically indistinguishable cryptic species, whose endosymbiont infection patterns often varied at the spatial and temporal dimension. However, the effects of ecological factors (e.g., climatic or geographical factors) on the distribution of whitefly and the infection frequencies of their endosymbionts have not been fully elucidated. We here analyzed the association between ecological factors and the distribution of whitefly and their three facultative endosymbionts (Cardinium, Hamilitona, and Rickettsia) by screening 665 individuals collected from 30 geographical localities across China. The study identified eight B. tabaci species: two invasive species, MED (66.9%) and MEAM1 (18.2%), and six indigenous cryptic species (20.9%), which differed in distribution patterns, ecological niches, and high suitability areas. The infection frequencies of the three endosymbionts in different cryptic species were distinct, and multiple infections were relatively common in B. tabaci MED populations. Furthermore, the annual mean temperature positively affected Cardinium and Rickettsia infection frequencies in B. tabaci MED but negatively affected the quantitative distribution of B. tabaci MED, which indicates that Cardinium and Rickettsia maybe play a crucial role in the thermotolerance of B. tabaci MED, although the host whitefly per se exhibits no resistance to high temperature. Our findings revealed the complex effects of ecological factors on the expansion of the invasive whitefly