The adverse effects of microplastics on microalgae species have been extensively studied, but their impact on the bait microalgae entering the food chain has not been well understood. This study investigated the cytological and physiological response ofIsochrysis galbanato polyethylene microplastics (PE-MPs, 10 μm) and nanoplastics (PE-NPs, 50 nm). The results showed that PE-MPs had no significant impact onI. galbana, while PsE-NPs obviously inhibited cell growth, reduced chlorophyll content, and caused a decline in carotenoids and soluble protein. These changes in the quality ofI. galbanacould negatively affect its use as aquaculture feed. To understand the molecular response mechanism ofI. galbanato PE-NPs, transcriptome sequencing was performed. The result revealed that the TCA cycle, purine metabolism, and some key amino acid syntheses were down-regulated by PE-NPs, while the Calvin cycle and fatty acid metabolism were up-regulated to tolerate PE-NP pressure. Microbial analysis showed that the bacterial community structure associated withI. galbanawas significantly altered at the species level by PE-NPs. In conclusion, this study provides new insights into the physiological stress response caused by microplastic pollution based on transcriptome and bacterial community analysis. The findings highlight the need to mitigate the release of microplastics into the environment to prevent their harmful effects on aquatic ecosystems and will be helpful in understanding the impact of polyethylene nanoplastics on the bait microalgae.