Large-scale crop monocultures facilitate the proliferation and increasing prevalence of diseases and pest insects.  Many studies highlight the impacts of plant diversification upon pathogens, and the population dynamics of insects and beneficial organism in agricultural ecosystems.  These studies provide evidence that habitat manipulation techniques such as intercropping, relay, and rotation can significantly improve disease and pest management.  This review introduces the concept of crop diversity, considers recent insights and mechanisms underlying crop diversity, and discusses its potential for improving sustainable agricultural practices.  Recently, the phytobiomes resulting from increased crop diversity are increasingly recognized for their contribution to disease and pest control.  Further, understanding the interactions between pathogens or pests with their host phytobiome may lead to novel options for the prevention of pests.  Recent advances in the agricultural systems include: (i) a better understanding of the mechanisms of interactions between crop species and genotypes; (ii) ecological progress including a better understanding of the context-dependency of those interactions; and (iii) the role of microtopographic variation in agricultural systems for priming basal resistance to multiple pests and pathogens by intercropped crops.  We also highlight recent progress in China and the potential options for habitat management and design that enhance the ecological role of biodiversity in agroecosystems.