Different kinds of freshwater fish soups show a diverse range of health functions, due to their different nutritional substances and corresponding bioactivities. In the current study, in order to learn the theoretical basis of the potential role fish soup plays in diet therapy functions, the changes of nutrient profiles and antioxidant activities in crucian carp soup and snakehead soup (before and after simulated gastrointestinal digestion) were investigated, such as chemical composition, free amino acids, mineral and fatty acid contents, DPPH radical scavenging activity, ferrous ion chelating activity, hydroxyl radical-scavenging activity and the reducing power effect. Results show that the content of mineral elements in snakehead fish soup was significantly higher than that of crucian carp soup, especially for the contents of Ca, Zn, Fe. The content of total amino acid (TAA) of crucian carp soup (82.51 mg/100 mL) was much higher than that of snakehead fish soup (47.54 mg/100 mL) (p < 0.05). Furthermore, the antioxidant capacity of crucian carp soup was stronger than that of snakehead soup. The intensive profiles of nutritional composition and antioxidant activities of these two kinds of fish soups were expected to partly provide the theoretical basis of therapeutic effects.