Based on the limited hepatic hydroxylation efficiency of dietary VD3 in teleosts and the superior bioavailability of its metabolite, 25(OH)D3, this study investigated the regulatory mechanisms of dietary 25(OH)D3 supplementation in yellow catfish—an economically significant species lacking prior nutritional data on this metabolite. A total of 360 fish were divided into three groups—control (basal diet), VD3 (2500 IU/kg VD3), and 25(OH)D3 (2500 IU/kg 25(OH)D3)—and fed for 8 weeks. Compared to the control, both supplemented groups showed elevated superoxide dismutase (SOD), total antioxidant capacity (T-AOC), catalase (CAT), and transforming growth factor-β (<i>TGF-β</i>) activities, alongside reduced malondialdehyde (MDA), interleukin-1β (<i>IL-1β</i>), and tumor necrosis factor-α (<i>TNF-α</i>) levels. The 25(OH)D3 group exhibited higher T-AOC and CAT activities and lower <i>TNF-α</i> than the VD3 group. Metabolomic and transcriptomic analyses identified 65 differentially expressed metabolites (DEMs) and 3515 differentially expressed genes (DEGs). Enrichment analysis indicated that the DEMs (e.g., indole compounds, organic acids, aldosterone, L-kynurenine) and DEGs (<i>pgd</i>, <i>mthfr</i>, <i>nsdhl</i>, <i>nox5</i>, <i>prdx2</i>, <i>mpx</i>, <i>itih2</i>, <i>itih3</i>, <i>eprs1</i>) that were highly and significantly expressed in the 25(OH)D3 group were primarily associated with antioxidant defense and inflammatory responses. Dietary 25(OH)D3 was more effective than VD3 in promoting antioxidant capacity and modulating inflammation in yellow catfish.