Bis-urea macrocycle 1 forms N-H···O= hydrogen-bonded one-dimensional (1D) channels, and the acetic acid (AcOH) dimer can be introduced into the 1D tubular channels, forming a 1D guest adsorption crystal (S1). The guest AcOH was easily desorped from the 1D channel to generate an empty 1D channel (S1′), which was further transformed into a thermodynamically stable two-dimensional (2D) hydrogen-bonding zigzag layer (S2) at temperatures above 520 K. The formation of host-guest molecular complexes with 1-dichloroacetic acid, tetrahydrofuran, pyrrole, pyridine, 3,4-difluoroaniline, and 1,4-diaminoalkanes was confirmed by X-ray crystal structural analyses, and molecular assembly structures of isolated monomers (S0), 1D channels (S1), 2D layers (S2), and dimeric 2D layers (S3), respectively, were observed depending on the size and shape of guest molecules. Guest desorption from the S0, S1, S2, and S3 assemblies resulted in a structural transformation to the thermodynamically stable guest-free S2′. Of these structures, a transformation from 1D guest-filled channel S1 to guest-free S1′ was observed for linear guests of (AcOH)2 dimers and NH2(CH2)nNH2 (n = 3, 5, and 7) with a molecular length longer than ca. 1 nm. The guest-filled 2D layer of S2 was transformed to S2′ after the guest desorption and also to S1 through AcOH readsorption, suggesting a reversible S1-S2′ structural transformation by stepwise thermal treatment and guest adsorption-desorption processes. Both the N2 and CO2 adsorption behaviors were not observed in thermodynamically stable S2′, whereas selective CO2 adsorption was confirmed in S1′.