The structural, electronic, and magnetic properties of transition metal atoms intercalated bilayer graphene, [GTMG] x/y , (x, y is integer, TM = Ti, Cr, Mn, Fe) with different TM/carbon hexagons ratios and insertion patterns, are systematically studied by density functional theory calculations. All the studied systems are thermodynamically stable and competitive ionic−covalent bonding characters are dominated in the TM−graphene interaction. Most studied systems are ferromagnetic; particularly, [GCrG] 1:1 8 , [GCrG] 1:9 , [GFeG] 1:6(1) , and [GTMG] 1:6(2) (TM = Cr, Mn, Fe) exhibit large magnetic moment of 4. 43, 5.60, 7.02, 10.85, 9.04, and 5.19 μ B per unit cell, respectively. In contrast, [GCrG] 1:8 and [GFeG] 1:8 are ferrimagnetic, while eight other [GTMG] x/y are nonmagnetic. Moreover, five intercalation nanostructures of [GTMG] 1:18 (TM = Ti, Mn), [GTMG] 1:9 (TM = Ti, Mn) and [GTiG] 1:6 are semiconductors with the gaps of 0.141/0.824 eV, 0.413/0.668 eV, and 0.087 eV, respectively. Comparison on different isomers with same TM/carbon hexagons ratios showed that the electronic and magnetic properties of these [GTMG] x/y are largely dependent on the TM atoms arrangement. For thus, an effective way to control the electronic and magnetic properties of graphene based nanostructures is proposed.