The aim of this study was to investigate the effect of polyethylene (PE), polyvinyl chloride (PVC) and polyhydroxyalkanoate (PHA) microplastics on greenhouse gas and ammonia emissions during 60 days composting. PE, PVC and PHA microplastics were respectively mixed with the cow manure; and a treatment without microplastics was used as the control. Compared to the control, PE and PVC inhibited organic matter degradation. Conversely, PHA accelerated temperature increases and organic matter degradation. Meanwhile, PE and PHA aggravated CH4 and NH3 emissions by 7.9–9.1% and 20.9–33.9%, respectively. PVC decreased CH4 and NH3 emissions by 6.6% and 30.4%, respectively. Additionally, the N2O emissions of the PE and PVC treatments were higher than those of the control while PHA decreased N2O emissions by 11.8%. Furthermore, PE, PVC and PHA microplastics reduced the NO3−-N contents and compost maturity. The results indicated that microplastics reduced compost quality while the effects of microplastics on greenhouse gases and ammonia emissions were related to their sources.