Engineered nanomaterials (ENMs), a kind of intentionally produced materials formed of particles varying from 1 to 100 nm in particle size, possess unique physicochemical properties that are not shared by any of their corresponding bulk materials. Due to their unique physicochemical properties, ENMs are getting more and more extensive in application to a wide range of technical fields in human production and life. Hence, it has become inevitable for ENMs to get released into the environment. ENMs enter into farmlands with ENM-containing pesticides, fertilizers and slurries from wastewater treatment facilities, posing potential risks to agricultural ecosystems. Being the essential components of an agricultural ecosystem, plants and soil microorganisms play critical roles affecting fate and transport of ENMs in the environment though adsorption, uptake and bioaccumulation. Therefore, how they affect plants and microorganisms ecologically attracts increasing attention from researchers the world over. Their researches may provide some valuable information to a better understanding of the consequences of introducing ENMs into ecosystems. Besides, as plants and microorganisms are closely related to each other, interact with each other and mutually influence each other, they form a plant-microorganism ecosystem. In this review, influences of ENMs on plants and microorganisms in the ecosystem are summarized. First, mechanisms of the potential ecotoxicities of ENMs and their relationships with the special properties of ENMs were collated and then researches of influences of ENMs on plants, soil microorganisms and plant-microorganism ecosystems were expounded. The review reveals that ENMs may have some impacts, varying in degree, on plant and microbes, and degree of the impact is related to kind of ENMs and species of the object and could be divided into three categories, negative, positive and insignificant. Moreover, researches have found plants and microbes may have some potentials to affect bioavailability of ENMs, which may serve as feedback to the ecological effect of ENMs on the plant-microorganism ecosystem. Recent studies on actual plant-microbe ecosystems found that ENMs affected functioning of arbuscular mycorrhizal fungi and azotobacters and excretion of iron chelator from soil microbes in the plant rhizosphere, thus altering eco-effect of ENMs, which suggests that to deem plants and soil microbes as an entity in the research may help the researchers go further in depth in studies on eco-effects of ENMs. Finally, the review lists out problems existing in the current researches with their pathways and techniques and focal points as well in ongoing researches.