A significant challenge in our time is to produce sufficient agricultural products on limited farmable land to meet the needs for food, feed, fiber, and industrial uses in the face of a changing climate. Conventional cropping systems mostly rely on inputs, such as fertilizers and pesticides, to boost crop yields. However, excessive inputs increase production costs and entail more direct and indirect emissions of greenhouse gases to the atmosphere that negatively impact the environment. Finding sustainable ways to increase crop productivity with little or no impact on the environment is the primary goal of modern agriculture. This review reveals that temporal-spatial diversification of crop rotations is critically needed to advance toward this goal sustainably. We find that (i) intensified crop rotations enhance carbon conversion from atmospheric CO2 into plant biomass and thus sequester more carbon into soil; (ii) diversified crop mixtures improve system resilience, i.e., increased resistance to pest/disease incidence and weed infestation, and faster recovery after removal of the abiotic or biotic stress; (iii) diversifying crop rotations increases crop yields at the system level with improved water and fertilizer use efficiencies; (iv) legume-based crop rotations reduce the need for synthetic nitrogen fertilizers thus lowering N2O and CO2 emissions to the atmosphere; (v) crop diversity leads to soil microbiome diversity that optimizes soil microenvironment, improving soil health. We believe that developing and adopting of diversified cropping systems are key factors for agricultural policy setting and a top priority for on-farm decision-making to increase crop productivity and enhance soil health, while reducing negative environmental impacts.