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The source strength and sink demand as well as their interaction have been demonstrated to co-regulate the synthesis of starch and determine the grain quality, but the knowledge of the underlying physiological mechanisms is limiting. An indica variety, Yangdao 6, and a japonica variety, Jinxiangyu 1, were planted with three treatments, including normal growth plant (CK), leaf-cutting (LC) and spikelet-thinning (ST). The transcript levels of starch metabolic genes, physicochemical characteristics of starch and appearance, milling, cooking and tasting qualities of rice under different treatments were determined. The ST treatment increased the relative expression of genes related to the synthesis of short branch-chains of amylopectin (SSI, BEI, BEIIb) and amylose (GBSSI) and reduced the relative expression of medium-long to long branch-chains of amylopectin synthesis genes (SSIIa, SSIIIa, SSIIIb, ISA1). When comparing ST with the CK treatment, starch granules became smoother with higher contents of short branch-chains and lower ratios of medium-long and long branch-chains of amylopectin; the crystallinity and the value of 1045/1022 cm−1 was decreased; for pasting properties, the setback and pasting temperature were decreased; the peak viscosity, hot viscosity, breakdown and final viscosity were significantly increased. Meanwhile, the ST treatment improved the appearance, milling and cooking and tasting qualities. The opposite results were observed under the LC treatment. These results indicated that source strength and sink size would regulate expression levels of starch metabolic genes, which is pivotal for the contents of amylose and short/long branch chains ratio of amylopectin, thus changing the structure and physicochemical properties of starch and grain quality. Here, we speculated that the improved source strength in terms of higher leaf/canopy photosynthesis and small sink size, such as small panicle size, would be preferred traits in high grain quality rice breeding.