Extended reality (XR) is a general term for virtual reality (VR), augmented reality (AR), and mixed reality (MR). By converting abstract digital expressions into intelligent feedback through figures, one can effectively compensate for the poor performance of traditional learning in deep cognitive processing and operational skills training. However, the extant results are uncertain, and only a limited number of studies have investigated the influence mechanism of heterogeneity among VR, AR, and MR on procedural knowledge learning, higher-level presence and generative cognitive processing, higher-quality operational behavior, and knowledge transfer. This study explored and analyzed the influence of XR heterogeneity on procedural knowledge gain and operation training. Participants (n = 127) were recruited from junior undergraduate students majoring in rail traffic signal and control. Based on the procedural disassembly and assembly of the ZD6 electric switch machine, an XR pretraining system and a 3-D-printed combined virtual-real procedural training system were developed to collect three types of data regarding knowledge gain, procedural training, and a set of questionnaires. Subsequently, a one-way analysis of variance was conducted with XR as the moderator variable. The results indicate that fully immersive VR is more conducive to procedural operation training; however, space and real factors must be considered. AR is consistent with the learner's operating habits, but the corresponding lack of immersion and interactivity restricts the improvement of procedural learning effects. MR multimodal perception leads to an increase in cognitive load, but moderate cognitive pressure is conducive to the cultivation of procedural cognition skills. Furthermore, this study proposes suggestions for using XR to intensify the perception and understanding of procedural cognitive actions.