Remote biopsy sampling (RBS) is an important method to obtain epidermal samples from free-ranging cetaceans. The efficiency and effect of different RBS tools on the targeted animals remain a concern for scientists. The Paxarms Mk24c Projector (PMP) biopsy system, designed especially for small cetaceans, has proven to be practical for several small cetacean species. In the present study, we used a PMP to collect epidermal samples from free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) distributed in coastal waters of the northern South China Sea to evaluate the efficiency and effectiveness of the PMP system and to assess any potential adverse impacts on Indo-Pacific humpback dolphins. Thirty-five tissue samples were obtained from 193 biopsy attempts, registering a sampling success rate of 18% in the present study. None of the dolphins that were targeted for biopsies (n = 193) using the PMP biopsy system showed any obvious adverse short-term reaction. Also, biopsy attempts, regardless of sampling success, did not significantly influence the targeted individual's reaction grade (p > 0.05). Similar to previous studies, sampling distances and Beaufort scales were key factors influencing sampling success. Based on the results of this study, we recommend that RBS on the Indo-Pacific humpback dolphin should be conducted within a distance of 25 m under sea state of Beaufort scale 3. A significantly higher sampling success rate was obtained when the animals were foraging and resting rather than travelling and socializing, regardless of different group sizes. The present study indicated a successful application of the PMP biopsy system for sampling from Indo-Pacific humpback dolphins in Chinese waters, and the PMP will contribute to studies relevant to Indo-Pacific humpback dolphin conservation for this vulnerable species throughout the world.