Nutritional and epidemiological studies suggest that the excessive intake of highly processed starchy foods contributes to the risk of type II diabetes and obesity in consumers. This is partly caused by the disruption of the cellular structure of cereal endosperms or legume cotyledons in foods during processing, which releases large amounts of highly digestible starch though the cell wall structure. Thus, to improve the production of starch-based foods with slowly digestible starch, it is necessary to clarify the influence of the structural integrity of cereal endosperm and legume cotyledon cells and the modification of their structure during processing on the starch digestion properties. However, the effect of mechanical, chemical, biological, or enzymatic modification of the cell wall during the processing of cereals and legumes on the digestive properties of starch has not been summarized well. Accordingly, in the present review, we fill this gap by summarizing the biophysical properties of common cereal and legume endosperm/cotyledon cells. Furthermore, we elaborate on the mechanisms involved in imparting cell wall integrity and controlling the starch digestion properties. Subsequently, the starch release pattern after cell wall modification is also discussed. In addition, a new classification system is proposed, which is beneficial for conducting cell research. This review provides new insights into the cell wall integrity of starch sources and the effect of the modification of cereal and legumes on starch digestion, which will benefit the scientific community and industry.