Abstract Urbanization has become a widespread social development trend in China. The size and configuration of urban built-up patches (UBPs) at a regional scale is presumed to be related to the extinction of rural and urban native plants in the landscape because of a tolerance threshold. The current study aimed to test the species area relationships in the heterogeneous space of UBPs vs. native plant taxa, which would enable examination of the tolerance thresholds of native plants to UBPs size and configuration. We investigated the types of land use, the patch configurations in the main region of Chongqing in western China, the statistics of native woody plants belonging to different species, and the life/growth forms found in sampling transects from four directions (east, west, north and south) along the rural-suburb-urban gradient. The size of UBPs has significant threshold effects on the native plant taxa, as well as the types of life/growth forms. Shrubs and deciduous plants are more resistant to the UBP size, followed by trees and evergreens. In addition, the smaller, more scattered, and rounder UBPs are related to more likely survival of native plants. The effect of the UBPs sizes in the landscape on native plants is negative, with critical thresholds ranging from 52.94% to 57.54% in a subtropical, mountainous megacity. Different plant taxa/life forms have different response thresholds. The influence of UBPs configurations on native plants can be positive or negative. The underlying mechanism of thresholds is thought to be caused by the accumulation of UBPs that form a matrix on the landscape.