Hot embossing is a manufacturing technique used to create microchannels on polymer substrates. In recent years, microchannel fabrication technology based on hot embossing has attracted considerable attention due to its convenience and low cost. A new evaluation method of microchannels, as well as an approach to obtaining optimal hot embossing conditions based on the Taguchi method, is proposed in this paper to fabricate precise microchannels for a flexible proton-exchange membrane fuel cell (PEMFC). Our self-made hot embossing system can be used to fabricate assorted types of micro-channel structures on polymer substrates according to various applications, whose bottom width, top width, height and cross-sectional area vary in the aims of different situations. In order to obtain a high effective filling ratio, a new evaluation method is presented based on the four parameters of channel structures, and the Taguchi method is utilized to arrange three main factors (temperature, force and time) affecting the hot embossing in orthogonal arrays, quickly finding the optimal condition for the embossing process. The evaluation method for microchannels proposed in this paper, compared to traditional evaluation methods, incorporates the area factor, providing a more comprehensive assessment of the fabrication completeness of the microchannels. Additionally, it allows for the quick and simple identification of optimal conditions. The experimental results indicate that after determining the optimal embossing temperature, pressure and time using the Taguchi method, the effective filling rate remains above 95%, thereby enhancing the power density. Through variance analysis, it was found that temperature is the most significant factor affecting the hot embossing of microchannels. The high filling rate makes the process suitable for PEMFCs. The results demonstrate that under optimized process conditions, a self-made hot embossing system can effectively fabricate columnar structure microchannels for PEMFCs.