The resource base that ensures food supply and the socio-economic component which depends on this resource base are the two major components that make up the food system in sub-Saharan Africa. The sequence of the food system is organized in a spatial flow framework of biomass base. The components of rural production system consist of food production biomass at homestead and farm level, and often at the communal base non-food production lands. The degree of integration between these resources base determines flows such as material cycle, energy, food and cash, and influences how the entire production system needs to be managed. The management system influences resource use efficiency and economic returns at different levels, at individual household, communities, and national levels. Efforts to developing agriculture and reducing poverty remained sectoral and focused mainly on a specific crop or individual animal level, failed to see interconnections among sub-systems and across space and time. The concept of the integrated food system has not been adequately adopted, in many sub-Saharan African countries and the agricultural system in the region continues to exhibit a low level of productivity and resource use efficiency. Hence, food insecurity and poverty remained high among smallholder farming communities producing crop and livestock despite the availability of arable land and abundance of another natural resource. This review focuses on the significance of integrated crop-livestock system in the tropics and suggests a framework to begin understanding and addressing complex problems in smallholders’ production system.