Methylparaben (MeP) is a ubiquitous pollutant in aquatic environment, which has caused severe pollution worldwide. However, aquatic toxicology of MeP is still largely unknown. In the present study, adult zebrafish were exposed to environmentally realistic concentrations of MeP (0, 1, 3, and 10 μg/L) for 28 days. In terms of the antimicrobial nature, dysregulation of gut microbiota and zebrafish health by MeP were elucidated after exposure. High-throughput amplicon sequencing showed that MeP subchronic exposure was able to disrupt the composition and diversity of gut microbial community, which was characterized by the alterations in alpha diversity and divergent distribution by principal component analysis. In addition, MeP exposure increased the body length and body weight of female fish, implying stimulated growth at low doses. In male intestine, consistent increases were notable in goblet cell density, tight junction protein (TJP) 2 expression, and serotonin neurotransmitter concentration after MeP exposure. In contrast, female intestine exposed to MeP had lower density of goblet cells, inhibited expression of TJP2, reduced concentration of serotonin, but up-regulated transcription of pro-inflammatory cytokine. Under the stress of MeP pollutant, intestinal catalase antioxidant enzyme was activated, thus contributing to the removal of oxidative free radicals. Correlation analysis verified the modulation of TJP2 expression by Lactobacillus probiotic bacteria. Disturbances in goblet cell, tight junctions, and serotonin by MeP may be combined to interfere with gut barrier function. Overall, the present study highlights the impairment of intestinal health by environmentally realistic concentrations of MeP, which necessitates an urgent risk assessment.