Ultrasonic imprinting uses ultrasonic vibration energy to replicate micropatterns on thermoplastic polymers. The ultrasonic imprinting process corresponds to the following mechanism: (i) microscale vibration of an ultrasonic horn causes repetitive deformation of polymer surface, (ii) the surface region of the polymer is locally softened by the repetitive deformation and friction, and (iii) micropatterns engraved on the horn or mold are replicated on the softened substrate. To replicate micropatterns with high dimensional accuracy, the effects of various processing conditions should be investigated, which have been studied through experimental observations so far. In this study, a coupled numerical analysis is performed to investigate heating mechanism of the ultrasonic imprinting process, by connecting transient structural and heat transfer analyses. Through the proposed coupled simulation, the effect of imprinting conditions on the replicated pattern quality is investigated. The difference of forward imprinting and backward imprinting is also discussed in terms of its heating mechanism and pattern replication characteristics.