A thermomechanical method was applied to study the topological and molecular structure of SKD butadiene rubber masticated and mixed with carbon black. Triblock structure (two amorphous blocks and one a pseudocrystalline structure) of a studied raw rubber and rubber compound networks were found. A ratio of these morphology structures changes during mastication. After mastication, a low-temperature block has two glass transition temperatures that shows its more complex structure than that in raw rubber. This shows deep transformations taking place during the mastication process. Despite applying high shear forces and heating during mixing with carbon black in a filled BR compound, we present three structures characteristic for BR. However, introduction of carbon black changes the topological structure of polybutadiene. A part of both amorphous blocks grows. A part of a crystalline structure lowers from 88% after 2.5 min of mixing to 54% after 20 min of compounding. The molecular weight distribution of the chains between the junctions of the network and parts of low-temperature and high-temperature amorphous blocks, and pseudocrystalline structures in architecture of the rubber network were also calculated.