Microplastic (MPs) pollution is a major global agroecosystem issue. Microplastic (≤ 0.2 μm) are mainly uptake by roots and transferred to the edible part of the crop, which also can be absorbed by the leaf. MPs and its extractum seriously impact crop growth and development, yield, and quality. We discuss the evidence and integrate omics studies to explore the adverse effects of MPs. The harmful impacts on crops mainly include decreasing crops’ germination and photosynthesis intensity, reducing crops’ biomass and the yield of edible parts, lipid peroxidation damage, changing in crop metabolic system, disrupting crop carbon and nitrogen metabolism, inducing chromosomal aberrations and DNA damage. In addition, MPs can change the species composition and community structure of soil root microorganisms, indirectly affecting crops’ growth and development. The toxicity depends on the materials type, particle size, and concentration of MPs. Crops can resist the toxicity of MPs by enhancing the antioxidant system’s function and generating more organic acids and other secretions from roots. We also analyzed the benefits and drawbacks of the current experimental methods used to study MPs’ effects on crops. Last, we point out the shortcomings existing in the research on the interaction between MPs and crops and put forward the direction and focus of future research. In the future, we should strengthen field experiments and consider the complex environment of soil. This review can offer a theoretical and scientific foundation for controlling and preventing MPs pollution in agro-ecosystem.