Crosscutting concepts (CCCs) are superordinate in the scientific concept system, common across disciplines, and very abstract. These characteristics, with the addition of incoherence in their curricular presentation, can challenge instructors. We designed a modular course based on coherence and conceptual understanding. The course structure was arranged in accordance with intra- and inter-unit coherence of CCCs, and each lesson was prepared according to “concept-based instruction” and the “5E instructional model.” The results of the pretest and posttest and the semi-structured interviews consistently showed that the participating high school students significantly improved their understanding of CCCs, thus supporting the effectiveness of the modular course.