Abstract: The characteristic of mandarin fish (Siniperca chuatsi) on live prey during the initial feeding stage poses challenges to artificial breeding and increases production costs. To evaluate the feasibility of replacing live prey and to investigate its effects on digestive function, 3 days post-hatch larvae were divided into two groups: a control group (HB) fed continuously with silver carp larvae, and an experimental group (AB) fed Artemia enriched with Schizochytrium from 3 to 6 days post-hatch, followed by silver carp larvae until 9 days post-hatch. Despite nutritional enrichment, the crude protein content of Artemia remained significantly lower than that of silver carp larvae. Growth performance was impaired in the AB group, with total length, specific growth rate (SGR), and survival rate (SR) all significantly reduced compared with the HB group. Except for pepsin, the activities of trypsin, lipase, and chitinase were significantly elevated in the AB group, indicating enhanced digestive stress. Histological examination revealed exfoliation and disorganization of the intestinal mucosa, shortened villi, and marked thickening of both intestinal walls and villi in the AB group. Transcriptomic analysis further demonstrated that differentially expressed genes in the AB group were enriched in immune- and apoptosis-related pathways, including IL-17, Toll-like receptor, TNF, NF-κB, and apoptosis signaling pathways. qPCR validation confirmed significant upregulation of key genes (il17ra1a, cxcl19, ccl20a.3, tnfb, casp7, casp10, and bax), aligning with transcriptomic trends. In conclusion, although nutrient-enriched Artemia may have short-term potential as an alternative initial diet, it can induce digestive stress and intestinal responses in mandarin fish larvae, thereby compromising growth and survival. This study provides useful references for optimizing feeding strategies at the initial stage and evaluating intestinal health in juvenile mandarin fish.