In order to elucidate the appropriate levels of microbial complexity in marine ecosystem models, the behaviors of community-based model including microbial diversity and three simpler models were compared, with focusing on the dynamics of particulate and dissolved organic carbon (POC and DOC) in the surface ocean. The strategy of the comparison was (1) to set parameter values of these four models so that they have the identical equilibrium at a specific environmental condition (here, the environment before the phytoplankton bloom) and then (2) to compare the non-equilibrium dynamics of these four models at another environmental condition (during the phytoplankton bloom). During the phytoplankton bloom, the ratio of bacteria-mediated POC decay rate and that of the DOC decay rate in simpler models to those in the community-based model ranged between 56% and 282%, and between 50% and 2872%, respectively. However, these differences resulted in much smaller variation in the net carbon fluxes; the ratio ranged between 77% and 128%. These damped impacts on carbon fluxes were due to the presence of competing processes in POC and DOC decay, i.e., zooplankton grazing and photochemical degradation.