In this study, a combination of experimental and statistical methods were employed to precisely determine the micro channel depth in ultra-thin metallic bipolar plates fabricated from 316 stainless steel with a thickness of 0.1 mm. The investigation centers on the rubber pad forming process and its role in the production of these critical components for Proton Exchange Membrane Fuel Cells (PEMFCs). To advance the understanding of this manufacturing process, experimental tests were designed using a Design of Experiment (DOE) technique and subsequently developed a predictive model using Response Surface Methodology (RSM). The research reveals a direct, quantifiable relationship between the channel depth in metallic bipolar plates and the magnitude of the applied force. Also, the pivotal role of rubber thickness as a dominant factor influencing channel depth was explored. Furthermore, it is revealed that augmenting the channel depth in these plates is attainable through a reduction in rubber hardness and an increase in rubber thickness. However, the benefits diminish once the rubber layer thickness exceeds a specific threshold. Moreover, the results underscore that the primary influential factors in this process include force, hardness, thickness, as well as the interplay between force and rubber thickness. The proposed model's accuracy is reaffirmed through an average error rate of approximately 5.39%, signifying its reliability in predicting microchannel depth. This research contributes novel insights into the manufacturing of ultra-thin metallic bipolar plates for PEMFCs, shedding light on the critical parameters influencing channel depth and their interrelationships. The significance and engineering value of this work lies in its potential for enhancing the design and manufacturing of metallic bipolar plates for PEMFCs. Precise control of microchannel dimensions is crucial for enhancing PEMFC performance and efficiency. This research not only advances clean energy technology but also contributes to the broader goal of achieving sustainable energy solutions, making it a noteworthy and timely contribution to the field.