The mechanism underlying the fragmentation of waxy maize starch (WMS) granules during high-pressure homogenization (HPH) was studied and the results were interpreted in terms of granular and molecular aspects. The diameter of disrupted starch granules decreased exponentially with increasing HPH pressure, but decreased linearly with increasing of HPH cycles. Scanning electron microscopy revealed a cone-like inside-out disruption pattern through the channels that resulted in separation of blocklets fragments or starch fragments. The Mw of amylopectin was reduced by ∼half following treatment at 150MPa with two cycles, or at 100MPa for eight cycles, and the decrease was in accordance with the disruption of starch granules. This indicated that amylopectin was “protected” by blocklets, and the disruption of WMS granules mainly occurred close to the linkage among blocklets. Increasing the HPH pressure appeared to be more effective for breaking starch granules than increasing the number of HPH cycles.