Interaction between wall and flow becomes more important when the scale of a channel decreases. We investigated two effects of wall presence for the transport of nanoparticle in a microchannel, which are the rarefaction effect up to early transient regime and hindered motion of nanoparticles. Lattice Boltzmann method coupled with Lagrangian nanoparticle tracking was used for modeling. Series of numerical simulation for various nanoparticle diameters, channel geometries, fluid velocities, and Knudsen numbers were performed. Some important features on nanoparticle transport such as capture efficiency, deposition velocity and deposition location were discussed. Using suitable dimensionless parameters, correlations for capture efficiency and deposition velocity were obtained. Considering hindered motion leads to significant decrease in the capture efficiency and deposition velocity. Results show that the effect of rarefaction on deposition is mostly because of varying the force acting on nanoparticles not due to slip velocity of fluid field near boundaries.