One of the main challenges in the transition to more sustainable agriculture is designing and selecting agricultural systems that are stable and perturbation resistant. Crop diversification is now recognized as a decisive part of sustainable agroecological development. It is one of the crucial agroecological practices that prove ecosystem services such as nutrient cycling, biological N fixation, pest and disease regulation, erosion control, climate regulation, soil fertility maintenance, biodiversity conservation, and carbon sequestration. To maximize these desired outcomes, understanding, designing, and optimizing, the adoption of crop diversification is crucial for the sustainability of food production under low-input practices. One approach to building sustainable food security and optimal management systems for limited resources is through the application of crop simulation models in multi-cropping systems. Indeed, some models can be used to simulate intercropping systems such as DSSAT, APSIM, ALMANAC, STICS, and FASSET. Thus, the application of such powerful models provides an option to redesign crop mixtures in appropriate sowing proportion and sowing date to tackle the enormous challenges facing agricultural development. In this regard, this review intended to assess existing suitable model to simulate multiple cropping systems and its role in building resilient crop production and ecosystem services without damaging the environment. It also highlights the key role of crop diversity as an ecosystem service provider to guarantee plant productivity in emerging systems of sustainable agriculture.