To investigate the effects of non-grain protein source and water temperature on growth and feed utilization differences of grass carp, the effects of different protein sources on the growth performance, serum biochemistry, digestive enzymes, amino acid transport and intestinal health of grass carp were studied at 24 °C, 28 °C and 32 °C. In this study, a total of 1350 grass carp (Ctenopharyngodon idella) (initial weight 5.00 ± 0.02 g) were selected, and Clostridium autoethanogenum protein (CAP), Tenebrio molitor meal (TMM), cottonseed protein concentrate (CPC) and Chlorella powder (CHP) were used as a single protein source to completely replace soybean meal for 56 days. The results showed that the final body weight (FBW), weight gain rate (WGR), specific growth rate (SGR) and protein efficiency ratio (PER) of grass carp increased significantly with the increasing temperature (P < 0.001). The CHP and SBM groups showed no significant differences in FBW, WGR, SGR and PER (P > 0.05), which were higher than the CAP, TMM and CPC groups (P < 0.001). The alanine transaminase (ALT), aspartate aminotransferase (AST), total protein (TP) and triglyceride (TG) concentrations of grass carp at 32 °C were significantly lower than those at 24 °C and 28 °C (P < 0.001). The acid phosphatase (ACP) activity decreased significantly with the increase of temperature (P = 0.001). The amylase (AMS) activity of the TMM, CPC and CHP groups was significantly lower than that of the SBM and CAP groups (P < 0.001), and the ACP and lipase (LPS) activities in the TMM group were significantly lower than those in the SBM group (P < 0.001). In addition, the interaction between temperatures and protein sources significantly affected the gene expression levels of amino acid transport including solute carrier family 1 member 3 (SLC1A3), solute carrier family 7 member 1 (SLC7A1), solute carrier family 7 member 5 (SLC7A5), solute carrier family 15 member 1b (SLC15A1b), solute carrier family 7 member 7 (SLC7A7), target of rapamycin (TOR), 4E binding protein 1 (4E-BP1) and ribosomal protein S6 kinase 1 (S6K1), intestinal inflammatory including tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-8 (IL-8), interleukin-10 (IL-10) and tight junction proteins (occludin, claudin1, claudin3, claudin7 and claudin11) (P ≤ 0.001). Collectively, our results indicated that CHP could be a potential protein source in the case of complete replacement of soybean meal in grass carp.