Background White feces syndrome (WFS) is a major health problem affecting intensive shrimp aquaculture, but its underlying mechanisms remain unclear. Increasing evidence suggests that WFS may involve complex interactions among host physiological status, intestinal microbial dysbiosis, and environmental microbial communities. However, the relationships among these factors within commercial shrimp culture systems remain poorly understood. Objectives This study aimed to investigate the associations among intestinal antioxidant capacity, intestinal microbiota, sediment microbial communities, and water quality parameters in Litopenaeus vannamei affected by WFS under small-pond culture conditions. Methods Healthy and WFS-affected shrimp were collected from a commercial shrimp farm in Zhanjiang, Guangdong Province, China. Intestinal antioxidant parameters, including total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and malondialdehyde (MDA), were determined. Intestinal and sediment microbial communities were analyzed using 16S rRNA gene sequencing. Water quality parameters and microbial community composition were compared between healthy and WFS groups. Results Compared with healthy shrimp, WFS-affected shrimp exhibited significantly increased intestinal MDA levels and decreased activities of T-AOC, SOD, and GSH-Px, indicating an imbalance in antioxidant status. Significant differences in intestinal microbial community composition were observed between groups, as confirmed by beta-diversity analysis (PERMANOVA, R 2 = 0.407, P = 0.022). WFS-associated microbial alterations included changes in dominant bacterial taxa and predicted microbial functional potential related to metabolism. The dominant taxa, referring to the most abundant microbial groups based on relative abundance, differed between healthy and WFS-affected shrimp. Sediment microbial communities also showed substantial compositional shifts, suggesting alterations in the surrounding microbial environment. In addition, nitrate and total nitrogen concentrations were significantly reduced in the WFS group. Conclusion These findings indicate that WFS occurrence is associated with coordinated alterations in shrimp antioxidant status, intestinal microbial structure, sediment microbial communities, and environmental conditions. This study provides new insights into WFS from a host–microbiota–environment interaction perspective and highlights potential indicators for monitoring shrimp health in aquaculture systems.