Evaluation of fish nutritional content information could provide essential guidance for seafood consumption and human health protection. This study investigated the lipid contents, fatty acid compositions, and nutritional qualities of 22 commercially important marine fish species from the Pearl River Estuary (PRE), South China Sea. All the analyzed species had a low to moderate lipid content (0.51–7.35% fat), with no significant differences in fatty acid profiles among fishes from different lipid categories (p > 0.05). Compared with previous studies from other regions, the examined fish species exhibited higher proportions of saturated fatty acids (SFAs, 39.1 ± 4.00%) and lower contents of polyunsaturated fatty acids (PUFAs, 21.6 ± 5.44%), presumably due to the shifted diet influence from increased diatoms and decreased dinoflagellate over the past decades in the PRE. This study further revealed that there was a significantly negative correlation between the trophic levels and levels of PUFAs in the examined species (Pearson’s r = -0.42, p = 0.04), likely associated with their differed dietary composition. Considering the health benefit of PUFAs, a few marine fish in PRE with low levels of PUFAs might have no significant contribution to the cardiovascular disease prevention, although fish with different fatty acid profiles most likely contribute differently towards human health. Additional studies are needed in order to comprehensively analyze the nutritional status of fish species in the PRE.