The cubic (Cub) phase structure of a thermotropic mesogen 1,2‐bis(4′‐n‐alkoxybenzoyl)hydrazine (BABH‐n, where n is the number of C atoms in the aliphatic tail) was examined by small‐angle X‐ray scattering. The BABH‐n system exhibits two types of Cub phases, Ia3d type and Im3m type. In the phase diagram as a function of the tail length (n) the Im3m‐Cub phase region (n = 13–16) was sandwiched by two Ia3d‐Cub phase regions with n < 13 and n > 16. On the basis of the triply periodic minimal surface (TPMS) picture, the Ia3d and Im3m structures are described by the gyroid (G) and doubled‐P (PP) surfaces, respectively. In this paper we focused attention on the internal structure of the Ia3d‐Cub phase at the molecular level. By examining how the relative intensity of the 220 reflection with respect to the 211 reference peak varies with n, we have successfully determined the position of the aliphatic tails, which are located on the G‐TPMSs. As far as we know, this is the first approach to clarifying the internal structure of the thermotropic Ia3d‐Cub phase. The usefulness of the systematic studies with respect to the tail length n has also been demonstrated.