Owing to overfishing, climate change, and environmental pollution, the biological and ecological characteristics of the small yellow croaker, Larimichthys polyactis in Haizhou Bay have greatly changed. In this context, the study of the trophic dynamics of the small yellow croaker in Haizhou Bay was conducted to provide a scientific basis for the sustainable use of the small yellow croakers. Bottom trawl surveys in Haizhou Bay and adjacent waters and the stomach content analysis of caught fish was conducted during the autumns of 2011 and 2013–2016. Based on the data collected, Hurdle-GAMMs (Hurdle-Generalized Additive Mixed Models) of the small yellow croaker in the Haizhou Bay ecosystem were built. The model combines the Hurdle model, Generalized Additive Mixed model, and mixed effect model, which can avoid the residual heterogeneity, non-independence, and sample grouping problems of GAM, and can be applied to the trophic dynamics of fish. The major prey species and key environmental factors were selected to examine the trophic dynamics of small yellow croakers. The results showed that predator length, distance from shore, and depth of water were the most important environmental factors for feeding in small yellow croakers. When the body lengths of small yellow croakers were between 80–100 mm and 120–140 mm, their feeding habits changed significantly. In addition, in areas 40–60 km offshore and at depths of 15–25 m, the food composition of small yellow croakers also changed significantly. The spatial variations of feeding in small yellow croakers were closely related to the distribution of prey species, and the variation in their feeding habits were also affected by multiple other factors. These were related to the spatial distribution of key prey species in the environment and interspecies relationships. In addition, the mouth crack, teeth, gill rake, and other feeding organs of small yellow croakers developed gradually with increases in body length. Therefore, the composition of key prey species will also change with increases in body length. In addition, the availability of prey could also affect the distribution of small yellow croakers and alleviate the interspecific competition in the Haizhou Bay ecosystem. The effects of various factors were also correlated with the feeding intensity in the small yellow croaker. Hurdle-GAMMs were proven to be an effective method for exploring the trophic dynamics of species and will provide theoretical support for the conservation and sustainable development of marine fisheries resources.