Lyme borreliosis, recognized as one of the most important tick-borne diseases worldwide, has been increasing in incidence and spatial extent. Currently, there are few geographic studies about the distribution of Lyme borreliosis risk across China. Here we established a nationwide database that involved
Borrelia burgdorferi
sensu lato (
B. burgdorferi
) detected in humans, vectors, and animals in China. The eco-environmental factors that shaped the spatial pattern of
B. burgdorferi
were identified by using a two-stage boosted regression tree model and the model-predicted risks were mapped. During 1986−2020, a total of 2,584 human confirmed cases were reported in 25 provinces.
Borrelia burgdorferi
was detected from 35 tick species with the highest positive rates in
Ixodes granulatus
,
Hyalomma asiaticum
,
Ixodes persulcatus
, and
Haemaphysalis concinna
ranging 20.1%−24.0%. Thirteen factors including woodland, NDVI, rainfed cropland, and livestock density were determined as important drivers for the probability of
B. burgdorfer
i occurrence based on the stage 1 model. The stage 2 model identified ten factors including temperature seasonality, NDVI, and grasslands that were the main determinants used to distinguish areas at high or low-medium risk of
B. burgdorferi
, interpreted as potential occurrence areas within the area projected by the stage 1 model. The projected high-risk areas were not only concentrated in high latitude areas, but also were distributed in middle and low latitude areas. These high-resolution evidence-based risk maps of
B. burgdorferi
was first created in China and can help as a guide to future surveillance and control and help inform disease burden and infection risk estimates.