Carbon nanotube (CNTs) networks embedded in a polymer matrix have been extensively studied as a flexible thermoelectric transport medium over the recent years. However, their power factor has been largely limited by the relatively inefficient tunneling transport at junctions between CNTs and the low-density conducting channels throughout the networks. This work demonstrates that significant power factor enhancements can be achieved by adding electrically insulating microscale particles in three-dimensional CNT networks embedded in the polymer matrix. When silica particles of a few µm diameters were co-embedded in single-walled CNT (SWCNT)polydimethylsiloxane (PDMS) composites, both the electrical conductivity and the Seebeck coefficient were simultaneously enhanced, thereby boosting the power factor by more than a factor of six. We found that the silica microparticles excluded a large volume of the composite from the access of CNTs and caused CNT networks to form around them with the polymer as a binder, resulting in improved network connectivity and alignment of CNTs. Our theoretical calculations based on junction tunneling transport for three-dimensional CNT networks show that the significant power factor enhancement can be attributed to the enhanced tunneling with reduced junction distance between CNTs. Additional power factor enhancement by a factor of three was achieved by sample compression, which further reduced the mean junction distance to enhance tunneling, but also reduced the geometric factor at the same time, limiting the enhancement of electrical conductivity.