Cannibalism is widespread in nature, but our understanding of its consequences and the underlying mechanisms remains so limited. Size structure within predator population can drive cannibalistic interactions and, as a results, it can modify roles of the predator population. Our field experiment using pond community involving cannibalistic Hynobius retardatus salamander larvae showed that when initial size variation of salamanders was large, the salamanders cannibalized more frequently and, thus, their abundance much reduced and the size variation increased due to greater growth of cannibals than non-cannibals. These cannibalism consequences provided contrasting effects on the salamanders’ top-down impacts to prey groups with different size. Compared to the non-cannibalistic situation, in the cannibalistic situation, small-sized prey (aquatic insect larvae) were exposed to lower predation pressure, but large-sized prey (Rana pirica frog tadpoles) were exposed to higher predation pressure from the salamanders. Hence, more aquatic insects but fewer frogs metamorphosed in the cannibalistic situations. Interplay between size structure and cannibalism of the salamanders can have profound consequences on pond community and energy flow from pond to terrestrial ecosystem.