Three novel 3D metal-organic frameworks of [Ni(2)(hfpdpt)(bpy)(2)(H(2)O)(2)](H(2)O)(8) (1), [Ni(3)(Hhfpdpt)(2)(bpy)(4)](H(2)O)(2) (2), and [Mn(2)(hfpdpt)(H(2)O)(2)] (3) have been synthesized by the hydrothermal reaction of Ni(II) or Mn(II) nitrate, 4,4'-(hexafluoroisopropylidene)diphthalic acid (H(4)hfpdpt), and 4,4'-bipyridyl (bpy). Complex 1 self-assembles into a 3D framework with unconventional 4-connected network topology, while 2 and 3 exhibit two kinds of unusual (4,8)-connected topological networks. Notably, in 1 and 2, the bpy coligand participates in the construction of their 3D frameworks, and the pH value also plays an important role to tune their space arrangements, while in 3, the bpy coligand is not involved in the final crystalline lattice. Furthermore, a detailed investigation on their magnetic and adsorptive properties is carried out.