Identifying the trophic role of primary producers is the basis of assessing seagrass bed functions but remains difficult due to the underdetermined analysis method. Here, we analyzed the multiple isotopes (δ13C, δ15N, and δ34S values) and fatty acid markers of food sources and macrobenthos in a tropical seagrass bed in summer and winter, and tried to combine these indicators to resolve the limitation of δ13C and δ15N values analysis. We found that the δ13C and δ15N values of epiphytes were like that of seagrass and macroalgae, while the δ34S values of epiphytes and macroalgae were significantly different, and the dominant unsaturated Fatty acid markers of seagrass (18:2n6c and 18:3n3) and epiphytes (16:1n7) were obviously different. These results suggest that the combination of multiple isotopes and Fatty acid markers can effectively distinguish the complex food source. In addition, we also found that multiple isotopes were more suitable to identify the food sources of polychaetes and snails with simple diets, fatty acids were more suitable to identify the food sources of crustaceans with complex diets, but their combination is essential in identifying the diets of macrobenthos since the wide range of isotopic values for omnivores crustaceans and the Fatty acid markers transformation during snails and polychaetes assimilation might mislead us when only isotopes or Fatty acid markers were used. Our findings suggest that in tropical seagrass beds, using multiple isotopes and fatty acid markers together can help reduce the uncertainty caused by single markers variation and thus strengthen the separation of food sources and the diets of different consumer species.