With the development of mobile sensors and biosensors, an ultrafine process technology that can generate ultrafine patterns and has mass production capability has garnered attention recently. Unlike the existing hot embossing techniques, the impact print‐type hot embossing process can generate a microscale pattern that has arbitrary pattern width and depth on a polymer film in real time using a single impact header. For this reason, this process can be applied to various industrial fields that require ultrafine patterns. However, it cannot create intricate patterns due to the limitations of the two‐axis stage control system. Furthermore, its application to a mass production that requires pattern repetition is limited because of the single header system. In this paper, a three‐axis impact print‐type hot embossing system using a multiheader and two algorithms, the impacting coordinate‐based data extraction algorithm and independent driving algorithm, to overcome the limitations of previous systems is proposed. Thanks to the multiheader and control algorithm, this process can generate repetitive patterns in real time, and it can adjust the pattern resolution by controlling the pattern extraction interval. The proposed method is thus expected to be widely applicable to industrial fields that require microscale user‐defined patterns such as mobile sensors and biosensors.