Bisphenol analogues (BPs) are ubiquitous pollutants to marine organisms as endocrine disruptive chemicals. However, the residue contamination and the trophic transfer of BPs in the apex predator nearshore dolphins are poorly studied. Here, we measured the concentrations of six BPs, including bisphenol A (BPA), bisphenol AF (BPAF), bisphenol B (BPB), bisphenol F (BPF), bisphenol P (BPP), and bisphenol S (BPS) in the liver of Indo-Pacific humpback dolphin (Sousa chinensis) (n = 75) collected from the Pearl River Estuary during a period with significant dietary changes (2004−2020). BPA and BPAF were the dominant components of the residue ∑BPs in the liver, with a proportion of 80%. Sex, maturity, and stranding location had no significant effects on BP levels. The generalized additive models indicated that BPA levels in juveniles and adults decreased from 2004 to 2013 while increasing from 2013 to 2020. The temporal trend of BPA levels was likely driven by the shift of the dominant diet from Harpadon nehereus to Thryssa spp. The concurrent increase of BPA loads in calves and juveniles and adults over the recent decades suggested that the diet-mediated variations of maternal BPA levels could be redistributed to their offspring.