The extensive use of bio-based plastics has led to their widespread distribution in the environment. However, their long-term ecological impact on aquatic animals is not well understood. In this study, adult zebrafish (Danio rerio) were exposed to 1000 items·L−1 of either polylactic acid (PLA) or polyethylene terephthalate (PET) microplastics (MPs), for 90 days. PLA is a typical bio-based plastic, while PET is a typical petroleum-derived plastic. The abundances of PLA and PET MPs in fish intestines were 981 ± 66 and 671 ± 151 items per fish, respectively, indicating a greater amount of PLA MP residues than PET MPs. However, the inhibitory effect of PET on fish weight was 1.8 times higher than that of PLA, suggesting energy compensation in PLA-treated zebrafish. Proliferation of Lactobacillus was observed in the fish intestines of the PLA group, indicating increased utilization capacity of intestinal flora for lactic acid production during PLA degradation. Metabolomics showed that the tricarboxylic acid pathway was up-regulated in the PLA group compared with that in the PET group, providing evidence of energy compensation. However, more ingested PLA MPs caused more significant histological damage to fish intestines than PET MPs. Therefore, the ecological risks of bio-based plastics still require attention.