Marine mesozooplankton play an important role for marine ecosystem functioning and global biogeochemical cycles. Their size structure, varying spatially and temporally, heavily impacts biogeochemical processes and ecosystem services. Mesozooplankton exhibit size changes throughout their life cycle, affecting metabolic rates and functional traits. Despite this variability, many models oversimplify mesozooplankton as a single, unchanging size class, potentially biasing carbon flux estimates. Here, we include mesozooplankton ontogenetic growth and reproduction into a 3-dimensional global ocean biogeochemical model, PISCES-MOG, and investigate the subsequent effects on simulated mesozooplankton phenology, plankton distribution, and organic carbon export. Utilizing an ensemble of statistical predictive models calibrated with a global set of observations, we generated monthly climatologies of mesozooplankton biomass to evaluate the simulations of PISCES-MOG. Our analyses reveal that the model and observation-based biomass distributions are comparable (r$_{pearson}$=0.40, total epipelagic biomass: 137TgC from observations vs. 232TgC in the model), with similar seasonality (r$_{pearson}$=0.25 for the months of maximal biomass). Including ontogenetic growth in the model induced cohort dynamics and variable seasonal dynamics across mesozooplankton size classes and altered the relative contribution of carbon cycling pathways. Younger and smaller mesozooplankton transitioned to microzooplankton in PISCES-MOG, resulting in a change in particle size distribution, characterized by a decrease in large particulate organic carbon (POC) and an increase in small POC generation. Consequently, carbon export from the surface was reduced by 10\%. This study underscores the importance of accounting for ontogenetic growth and reproduction in models, highlighting the interconnectedness between mesozooplankton size, phenology, and their effects on marine carbon cycling.