In this study, we examined the sensitivity of embossed pattern depth to preheat supply and cooling and investigated how the pattern type and density affect the embossed depth. The main factors that affect embossed pattern qualities of roll-to-roll hot embossing, such as roller temperature, roller speed, and applied force, were determined using the response surface methodology. Eight conditions were then added to determine the time-dependent effects of heat transfer with custom-designed preheating and cooling systems. An extended preheat time for the polymethylmethacrylate substrate contributed to the significant change in the embossed depth, whereas the substrate-cooling did not exhibit a clear increasing or decreasing trend. Larger embossed depths were achieved in the horizontal patterns with lower density than in the vertical patterns, and the lower pattern densities showed greater embossed depths in most embossing conditions. We expect that this result will help to understand the effects of the pre- and posttreatment of roll-to-roll hot embossing by employing time duration factors of heat transfer, depending on the mold pattern type and density.