Mixotrophic flagellates play an important role in connecting the classical food chain and microbial food loop. The feeding characteristics of the mixotrophic flagellate Poterioochromonas malhamensis have been well studied, but its role as a food source for other large zooplankton is less studied. This study focuses on the physiological and biochemical changes in P. malhamensis when using autotrophy, chemoheterotrophy, and phagotrophy, and the effect of these changes on the feeding ability of one of its predators, the ciliate Paramecium caudatum. The results showed that chemoheterotrophic P. malhamensis had a higher growth rate and larger cell size than autotrophic and phagotrophic P. malhamensis. The biochemical composition of P. malhamensis also varied greatly between the three nutritional modes. The protein, total absolute amino acid, and fucoxanthin contents were highest for autotrophic P. malhamensis, while chemoheterotrophic P. malhamensis had the highest contents of total sugar and total absolute fatty acid. The contents of most biochemical components in phagotrophic P. malhamensis fell between those in autotrophic and chemoheterotrophic P. malhamensis. A feeding experiment showed that the grazing ability of P. caudatum on chemoheterotrophic P. malhamensis was significantly higher than that on phagotrophic P. malhamensis and autotrophic P. malhamensis. This study showed that the transformation of nutritional modes can alter the biochemical composition of the mixotrophic flagellate P. malhamensis and, as a result, affect the grazing ability of its predator P. caudatum.