Although previous studies have confirmed the various benefits of concept maps, limited information is available regarding how to effectively employ the concept map in online courses. In this research, we have designed and assessed the effectiveness of the "Zoom-sandwiched cross-chapter concept map" model in an online biology course. The model has optimized the concept map project because it incorporates synchronous interaction as well as asynchronous communication among students, assigns required meetings with flexible schedules, endows students with intrinsic motivation, and is facilitated by indirect instructor intervention. Our results showed improved student skills in constructing the cross-chapter concept map and positive student perceptions of the model. In addition, this study provided an in-depth analysis of how students benefit from cross-chapter concept maps. Our findings could guide educators on how to optimize the concept map project and utilize concept maps effectively to overcome some primary learning challenges and enhance student learning in online education, especially in STEM fields.