Multi-rotor drones have expanded their range of applications, one of which being search and rescue (SAR) missions using infrared thermal imaging. This paper addresses thermal target tracking with track segment association (TSA) for SAR missions. Three types of associations including TSA are developed with an interacting multiple model (IMM) approach. During multiple-target tracking, tracks are initialized, maintained, and terminated. There are three different associations in track maintenance: measurement–track association, track–track association for tracks that exist at the same time (track association and fusion), and track–track association for tracks that exist at separate times (TSA). Measurement–track association selects the statistically nearest measurement and updates the track with the measurement through the IMM filter. Track association and fusion fuses redundant tracks for the same target that are spatially separated. TSA connects tracks that have become broken and separated over time. This process is accomplished through the selection of candidate track pairs, backward IMM filtering, association testing, and an assignment rule. In the experiments, a drone was equipped with an infrared thermal imaging camera, and two thermal videos were captured of three people in a non-visible environment. These three hikers were located close together and occluded by each other or other obstacles in the mountains. The drone was allowed to move arbitrarily. The tracking results were evaluated by the average total track life, average mean track life, and average track purity. The track segment association improved the average mean track life of each video by 99.8% and 250%, respectively