Synthesis of new zeolites involving organic molecules relies heavily on the trial-and-error approach, because it is difficult to interpret the determining effects of organics on zeolite crystal symmetry. Here, the intrinsic relationships among the space-filling of organics, included volume of channels, and zeolite crystal symmetry, are systematically demonstrated by experimental and computational means. Under controlled conditions, the dimer and monomer organics of 1-ethyl-3-methylimidazolium selectively direct different, but related, germanosilicates, the ECNU-16 with a new topology and the existing IM-16 with the UOS topology, respectively. The comprehensive computational study reveals that the zeolite phase selectivity is determined by the unique space-filling behavior of the dimer and monomer organics, which is closely correlated to their rotation freedom, as well as the included volume of host zeolite channels. The elucidation of this crucial space-filling effect from the fundamental viewpoint will provide new guidelines for the rational design and synthesis of new zeolites in future.