Metal-organic framework nanoparticles (MOF NPs) have received much attention for their potential use in nanopesticides. However, little is known about the potential health and environmental risks associated with these materials. In this study, the toxicological responses of zebrafish exposed to five MOF NPs for short and long periods of time were evaluated. The acute toxicity results showed that the toxicity of the five MOF NPs to zebrafish embryos and adult zebrafish was in the order of Cu-MOF > ZIF-90 > ZIF-8 > Fe-MOF > Zr-MOF. Histopathological analysis revealed that ZIF-8, ZIF-90, and Cu-MOF NPs caused liver swelling and vacuolization in zebrafish. The cellular ultrastructure showed that ZIF-8, ZIF-90, and Cu-MOF NPs severely damaged the mitochondrial structure in intestinal epithelial cells and liver cells. The 16S rDNA sequencing data showed that all five MOF NPs significantly altered the dominant microorganisms in the zebrafish intestine. The microbial markers of intestinal inflammation, Proteobacteria (Aeromonas, Plesiomonas, and Legionella), were significantly increased in the Fe-MOF, ZIF-8, Zr-MOF, and Cu-MOF treatment groups. Metabolomics results indicated that the levels of inflammatory promoting factors (Leukotriene E4, 20-hydroxyeicosatetraenoic acid) in arachidonic acid metabolism were decreased, and the levels of inflammatory suppressing factors (8,9-epoxyeicosatrienoic acid) were increased. Metabolites related to oxidative stress, such as glutamine, pyridoxamine, and l-glutamic acid in vitamin B6 metabolism and other signaling pathways, were significantly reduced. Overall, these results suggest that the different MOF NPs had widely varying toxicity to zebrafish, and further attention should be paid to the toxicity of MOF NPs in the real environment.