Pine wilt disease (PWD), caused by pine wood nematode (PWN), poses a tremendous threat to global pine forests because it can result in rapid and widespread infestations within months, leading to large-scale tree mortality. Therefore, the implementation of preventive measures relies on early detection of PWD. Unmanned aerial vehicle (UAV)-based hyperspectral images (HSI) can detect tree-level changes and are thus an effective tool for forest change detection. However, previous studies mainly used single-date UAV-based HSI data, which could not monitor the temporal changes of disease distribution and determine the optimal detection period. To achieve these purposes, multi-temporal data is required. In this study, Pinus koraiensis stands were surveyed in the field from May to October during an outbreak of PWD. Concurrently, multi-temporal UAV-based red, green, and blue bands (RGB) and HSI data were also obtained. During the survey, 59 trees were confirmed to be infested with PWD, and 59 non-infested trees were used as control. Spectral features of each tree crown, such as spectral reflectance, first and second-order spectral derivatives, and vegetation indices (VIs), were analyzed to identify those useful for early monitoring of PWD. The Random Forest (RF) classification algorithm was used to examine the separability between the two groups of trees (control and infested trees). The results showed that: (1) the responses of the tree crown spectral features to PWD infestation could be detected before symptoms were noticeable in RGB data and field surveys; (2) the spectral derivatives were the most discriminable variables, followed by spectral reflectance and VIs; (3) based on the HSI data from July to October, the two groups of trees were successfully separated using the RF classifier, with an overall classification accuracy of 0.75–0.95. Our results illustrate the potential of UAV-based HSI for PWD early monitoring.