Abstract: The scope of wild animal activities overlaps significantly with human production and living spaces, which leads to frequent incidents of wildlife damage. Especially in communities and farmers near nature reserves, which are more affected by the invasion of wild animals. Therefore, to alleviate the contradiction between wildlife conservation and agricultural production, and to coordinate the relationship between wildlife conservation and agricultural production. This study took the Chinese water deer (Hydropotes inermis) in the Yancheng Wetland Rare Bird National Nature Reserve in Jiangsu Province as an example. Based on the small animal tracking device (model HQAN40-S) equipped with 20 adult deer released from April 3, 2020 to April 28, 2022, 33 001 valid deer activity GPS point data were obtained. This study used the recorded GPS-GSM point data of deer, based on Kernel Density Estimation model, Principal Component Analysis, Vanderloeg selectivity coefficient and Scavia selectivity index, to reveal the characteristics of deer habitat selection and its impact on agriculture, and analyze the correlation between the damage caused by deer habitat selection and farmers’ willingness to protect. The results showed that deer prefer reed (Phragmites australis) swamp habitats for their habitat selection. In autumn, deer preferred to operate in areas with vegetation coverage less than 40%. In summer, deer did not choose to operate in areas with vegetation heights of 1 m to 2 m, and in winter, deer did not choose to operate in areas with vegetation heights less than 1 m. In addition, deer preferred to move within 50 m of farmland and open water habitats, away from roads and residential areas. The deer showed a clear preference for farmland in different seasons. In spring and summer, they preferred to choose farmland in the northern buffer zone, with a distribution area of 1 352.60 hm². This results in direct economic losses of 3 960 yuan/hm² and indirect losses of 74 580 yuan for rice (Oryza sativa) in summer. The distribution area of deer in farmland was relatively small during autumn and winter seasons. The direct economic losses or production disturbances caused by deer activities in farmland had a significant negative impact on farmers’ willingness to protect, and would greatly weaken their willingness to protect. When farmers had a high level of awareness of the value of deer, their willingness to protect deer would significantly increase. Policy makers should attach importance to the effectiveness of compensation mechanisms and enhance public education as an effective way to increase participation in conservation, which could effectively enhance farmers’ willingness to protect and reduce economic losses caused by wildlife damage.