Studies were done to understand the effects of polyamide 12 (PA 12) incorporation on microphase separation (microsegregation) in thermoplastic polyurethanes (TPU) based on oligoether (polytetramethylene oxide, molecular weight, 1000) and oligoester (polyethylene butylene glycol adipate, molecular weight, 2000), and relaxation transitions, compatibility, and molecular interaction energy in polymer blends. It was learned that the addition of PA 12 caused partial degradation of the domain structure in the oligoester-containing polyurethane, whereas interaction of hard blocks in the oligoether-containing polyurethane increased. Analyzing compatibility and interphase interactions in blends is possible in the frame of the quantum theory of relaxation processes. Also, interferences of the components on characteristic temperatures of relaxation transitions were studied. Partial compatibility was detected between PA 12 and the soft block of oligoether-based TPU over the whole range of components concentrations tested. For oligoester-based TPU, partial compatibility was observed only at low polyamide concentrations (up to 20 wt %). Effects of a polyurethane phase on PA 12 crystallization in the blends along with the pattern of concentration-mechanical properties dependencies are discussed.