The healthy development of the ecosystem and tourism in destinations plays an essential role in sustainable development. Taking Shennongjia as an example, we analyzed the spatial–temporal variation in the ecosystem services value (ESV) and investigated the impacts of tourism on ESV and their spatial heterogeneity using the geographically weighted regression (GWR) and boosting regression tree (BRT) models. The results showed that (1) the types of ecosystem services (ESs) were dominated by climate regulation and biodiversity. The ESV increased from 3.358 billion yuan to 8.910 billion yuan from 2005 to 2018 and showed significant spatial divergence, maintaining a long-term distribution pattern of high in the center and low at the border. (2) The GWR and BRT results showed that the Distance to Scenic Spots (DSS) and the Distance to Residential Areas (DRA) are important factors influencing ESV, with the Distance to Hotels (DH) and the Distance to Roads (DR) having a relatively weak influence on ESV. (3) The influencing factors presented positive and negative effects, and the degree of influence has spatial heterogeneity. The DRA and DH inhibited the increase in ESV in nearby areas, while DR was the driving factor for increasing ESV. The assessment results of DSS vary according to the models.