We demonstrate the rheological percolation of carbon nanotubes (CNTs) in microstructured polymer matrices. Polymer/CNT composites are fabricated from polycarbonates with different molecular weights to diversify the microstructures, which vary with the polymer radius of gyration and entanglements. We propose a model for the dispersion of CNTs in polymer matrices, which explains the electrical and rheological properties. The percolation theory represented by a power-law relation cannot account for the rheological percolation of CNTs in this work. Therefore, we investigate the crossover points to provide a quantitative indication of the rheological percolation threshold of nanofillers in polymer matrices. For the first time, the rheological percolation threshold is determined experimentally with this definition. The effects of molecular weight and shear viscosity of the medium on the percolation of CNTs are demonstrated separately.