We assessed habitat use by the population of Indo-Pacific humpback dolphin, Sousa chinensis, in the waters off Zhanjiang, China, by performing boat-based surveys between 2013 and 2018. In total, we gathered 253 sightings of humpback dolphins. To assess habitat use of humpback dolphins within the study area, we measured two spatial metrics at each sighting site: WD_T (tide-calibrated water-depth) and DS (distance to the nearest shore). Results showed that dolphins mainly were observed in shallow (WD_T: 8.46 ± 5.13 m, mean ± SD) and inshore (DS: 2.17 ± 2.14 km) waters. Their preference of inhabiting shallow waters was more apparent during the wet season (April–September) than during the dry season (October–March); however, they were encountered in waters much closer to shore during the dry season than the wet season. By weighting survey effort, our sighting density maps further confirmed that humpback dolphins changed their habitat use between wet and dry seasons. Such spatiotemporal variations in dolphin habitat use might be associated with spatiotemporal movements of their prey. Our findings provide insights into variations in fine-scale habitat use of inshore apex predators, and also assist to designate proper conservation measures for these vulnerable animals.