<p>Cetaceans play a crucial role in marine ecosystems, but many whale species are currently endangered due to human activities. The rise of whale watching as a non-extractive, conservation-oriented activity has raised concerns about its impact on cetaceans. Although a total of 40 cetacean species are distributed throughout Chinese waters, whale watching is still an emerging sector. This study aimed to evaluate the positive and negative effects of the development of the whale watching industry and establish guidelines for sustainable whale watching tourism in China. Boat-based observational surveys and historical sighting records were analyzed using Jolly-Seber open mark-recapture models to identify suitable species and priority regions. The Indo-Pacific humpback dolphin and Bryde’s whale emerged as suitable targets, and the Pearl River Estuary and the Beibu Gulf were highlighted as the most favorable whale watching sites. Eco-friendly guidelines were then formulated to minimize potential disturbances. The initiative represents a significant milestone in marine biodiversity conservation and sustainable tourism promotion in China, setting a precedent for responsible whale watching practices. Continual adjustment of guidelines based on the latest survey data is recommended to ensure long-term conservation efforts.</p> Graphical Abstract <p></p>