Nanoparticles (NPs) are widely used to tune the mechanical and physical properties of carbon nanotube (CNT) networks in many practical applications. However, the distribution of NPs in CNT networks and their effects on microstructural evolutions and mechanical properties remain elusive. We employed the coarse-grained molecular dynamics (CGMD) simulations to systematically investigate these issues. First, we found that compared to ambient temperature and the frequency of cyclic loads, the relative cohesion energy of NPs and strain amplitude of cyclic loads are more important factors for controlling the aggregation of NPs; it was also revealed that NPs with larger relative cohesion energy and in larger-strain cyclic loads would aggregate more severely in CNT networks. Second, we observed that the Young's modulus and the tensile strength of the material can be increased by up to ∼3.2 and ∼2.0 times, respectively, at the critical volume fraction of NPs (∼21.6%). Finally, the underlying mechanisms by which NPs strengthen the inter-tube joints and constrain the bundling of CNTs are unveiled. These results should be useful for the optimal design of CNT-based advanced materials.