Two 3D supramolecular isomers with composition Co2(BDC)2(BPNO) (BPNO = 4,4'-bipyridyl N,N'-dioxide, BDC = 1,4-benzenedicarboxylic acid) were prepared by using mixed ligands in different solvents. The two compounds are built up from different infinite chains of corner-sharing CoO6 octahedra. In compound 1, 2D CoBDC layers are pillared by neutral BPNO to form a 3D framework, while in compound 2, the interconnection between the zig-zag CoO chains and two organic moieties leads to a Co-based MIL-53 analogue containing 1D nanosized rhombic channels. Compound 1 is a weak ferromagnet with two field-induced magnetic transitions, and compound 2 displays antiferromagnetic interactions. Furthermore, compound 1 shows a typical solvatomagnetic effect and its desolvated compound appears to be a hidden weak ferromagnet with two field-induced magnetic transitions. The structural variation between compounds 1 and 2 is ascribed to the different hostguest interactions within the two compounds and is believed to be responsible for the difference in the magnetic properties. As a result of their identical framework composition, compounds 1 and 2, after removal of the guest molecules, exhibited similar gas adsorption behavior.