Existing individual size distribution (ISD) theories assume that the trophic level (TL) of an organism varies as a linear function of its log-transformed body size. This assumption predicts a power-law distribution of the ISD, i.e., a linear relationship between size and abundance in log space. However, the secondary structure of ISD (nonlinear dome shape structures deviating from a power-law distribution) is often observed. We propose a model that extends the metabolic theory to link the secondary structure of ISD to the nonlinear size-TL relationship. This model is tested with empirical data collected from a subtropical reservoir. The empirical ISD and size-TL relationships were constructed by FlowCAM imaging analysis and stable isotope analyses, respectively. Our results demonstrate that the secondary structure of ISD can be predicted from the nonlinear function of size-TL relationship and vice versa. Moreover, these secondary structures arise due to (1) zooplankton omnivory and (2) the trophic interactions within microbial food webs.