Ocular drug delivery is a complex and challenging process and understanding the transport characteristics of drug-loaded particles is very important for designing safe and effective ocular drug delivery devices. In this paper, we investigated the effect of the microchannel configuration of the microdevice, the size of drug-loaded nanoparticles (NPs), and the pressure gradient of fluid flow in determining the maximum number of NPs within a certain outlet region and transportation time of drug particles. We employed a hybrid computational approach that combines the lattice Boltzmann model for fluids with the Brownian dynamics model for NPs transport. This hybrid approach allows to capture the interactions among the fluids, NPs, and barriers of microchannels. Our results showed that increasing the pressure gradient of fluid flow in a specific type of microchannel configuration (tournament configuration) effectively decreased the maximum number of NPs within a certain outlet region as well as transportation time of the drug loaded NPs. These results have important implications for the design of ocular drug delivery devices. These findings may be particularly helpful in developing design and transport optimization guidelines related to creating novel microchannel configurations for ocular drug delivery devices.