In order to evaluate the effects of the interaction between different proteins and feeding frequency on largemouth bass (Micropterus salmoides) and to provide scientific guidance for the application of novel proteins and the corresponding optimal feeding strategy, a two-factorial design (5 × 3) with five protein feeds (fishmeal (FM), Clostridium autoethanogenum protein (CAP), Tenebrio molitor (TM), Chlorella meal (ChM), cottonseed protein concentrate (CPC)), and three feeding frequency (1, 2, and 3 times/d; FF1, FF2, FF3) was designed in culturing largemouth bass (initial weight, 2.98 ± 0.22 g/fish) for 8 weeks. Z-score combined with cluster analysis was used to analyze and compare the effects of different treatments on different indicators, such as growth performance, feed utilization, antioxidant capacity, and immune response to draw a general picture of the relationship among all these massive biomarkers. The results showed that different protein sources and feeding frequencies had significant interactive effects on growth performance, feed utilization efficiency, body lipid, and health status of largemouth bass. Fish fed with ChM feed showed similar performance to that in FM group, implying its potential for complete replacement of fishmeal in largemouth bass. Fish fed with CAP, TM, and CPC feeds showed worse performance compared to FM and ChM groups, characterized by poor growth and feed utilization, enhanced stress, chronic inflammation, and varying symptoms of histological changes in the liver and intestine, which demonstrated the adverse effects of the complete replacement of fishmeal by these three proteins. In terms of feeding frequency, fish fed with FM feed in FF3 group led to liver hypertrophy, fat accumulation, and the risk of fatty liver, while inducing liver inflammation. In addition, the TM and CAP group had the higher expression levels of inflammatory factors at FF3 group, which displayed that the interactions between FM, CAP, TM feeds and feeding frequency at FF3 might aggravate the occurrence of liver inflammation and oxidative damage of hepatocytes. Overall, FF2 had higher feed efficiency, protein efficiency, antioxidant enzyme and lysozyme activities, lower MDA content, and lower gene expression of inflammatory cytokines and could be considered as the optimum feeding frequency for largemouth bass fed with different protein feeds.