In recent years, consumers have shown a growing interest in purchasing welfare-friendly livestock products. Environmental enrichment has emerged as an effective approach to enhancing animal welfare. Based on this, this study aims to investigate the effects of welfare housing systems incorporating environmental enrichment on growth performance, meat quality, and intestinal health in rabbits. Rabbits were assigned into three groups: Cage group (Cage), Pen group (Pen), and Pen + environmental enrichment material group (PE). The Pen group exhibited a lower average daily weight gain and a higher feed conversion ratio. However, the meat color and nutrient content of the leg muscles were improved in both the Pen and PE groups to varying extents. Furthermore, fatty acid β-oxidation in the leg muscles was elevated in the Pen group, resulting in reduced lipid deposition. Additionally, both the Pen and PE groups displayed altered cecal microbiota composition and increased short-chain fatty acids content, contributing to enhanced intestinal health through the activation of G protein-coupled receptors. In conclusion, these findings suggest that the two welfare housing systems can improve meat quality and intestinal health. This study offers a theoretical foundation for welfare-oriented rabbit farming and the production of healthier rabbit meat to meet consumer demands.