Tick-Borne Encephalitis (TBE) is an important epidemic disease in the northern hemisphere, especially in Russia which has the longest history of suffering from the disease. In this study, logistic regression model is established combining both nature environment and socioeconomic factors to explore their impact on TBE incidence level. We found that education index, LPI (largest patch area explore index), urban land area, NDVI (normalized difference vegetation index), TBE incidence in the previous year acted as the promoting factors for increasing TBE incidence, whereas annual minimum temperature and social welfare represented by life expectancy years acted as hindering factors. The promoting risk of education index, LPI index, urban land area, NDVI, TBE incidence in the previous year decreased as time went by, but hindering factors, like social welfare, annual minimum temperature, were not observed significant change. Overall, among natural environment factors, urban land area and followed by forest fragmentation greatly affected the presence and the degree of TBE incidence, while among social economic factors, education index played significant roles. The incidence in the previous year also impacted the occurrence and the level of the TBE in most regressions. Attention should be paid on the forest fragmentation level on TBE control, and the incidence of previous years can be used as an indicator for TBE early warning.