This study aimed to assess the effects of different dietary vitamin D3 (VD3) levels on growth and carcass performance, tibia traits, meat quality, and intestinal morphology of yellow-feathered broilers. One-day-old broilers (n = 1440) were assigned into four treatment groups with six replicates per group, and each replicate contained 60 chicks. Dietary VD3 significantly improved the growth performance and carcass traits of broilers, and only low-dose VD3 supplementation decreased the abdominal fat percentage. High-dose VD3 supplementation improved intestinal morphology in the finisher stage, while the b* value of breast muscle meat color decreased markedly under VD3 supplementation (p < 0.05). Serum Ca and P levels and the tibia composition correlated positively with dietary VD3 supplementation at the early growth stage. The weight, length, and ash contents of the tibia increased linearly with increasing dietary VD3, with maximum values achieved in the high-dose group at all three stages. Intestinal 16S rRNA sequencing and liver transcriptome analysis showed that dietary VD3 might represent an effective treatment in poultry production by regulating lipid and immune-related metabolism in the gut–liver axis, which promotes the metabolism through the absorption of calcium and phosphorus in the intestine and improves their protective humoral immunity and reduces infection mortality. Dietary VD3 positively affected the growth—immunity and bone development of broilers during the early stage, suggesting strategies to optimize poultry feeding.