In this study, the fundamental issue of “how various functional molecules can be homogeneously and densely arrayed in a solid material” is addressed using discrete self-assembly of guest molecules with an orthogonal architecture (1) comprising hydrogen bonds; this method has become a new paradigm for constructing functional materials. The serendipitous finding of cocrystallization in 1 was prompted by its unexpectedly tight but transmutable inclusion of guest molecules. Notably, the self-assembly of 1 with imidazole molecules produced a water-durable, heat-resistant, one-dimensional (1D) anhydrous proton-conducting channel with proton-transfer sites in very close proximity (N–N distance, 2.481 Å). The close sites lead to faster proton transfer when compared with pure imidazole; this advantage via the close sites is attributable to wobbling rather than rotational motion. These results suggest that discrete self-assembly can enable the development of new design concepts for functional materials.