Two novel dioxidomolybdenum(VI) complexes [MoO2L′1] (1) and [MoO2L′2] (2) containing the MoO22+ motif with unexpected coordination motifs due to ligand rearrangement through Mo‐mediated interligand C–C bond formation are reported. The ligands (H2L′1–2) are tetradentate C–C‐coupled O2N2‐donor systems formed in situ during synthesis of the complexes by reaction of [MoVIO2(acac)2] with Schiff base ligands of 2‐aminophenol with 2‐pyridinecarbaldehyde (HL1) and 2‐quinolinecarbaldehyde (HL2). To confirm that the ligand rearrangement is assisted by molybdenum, the corresponding vanadium complexes [VO2L1] (3) and [VO2L2] (4) containing original Schiff base ligand (HL1,2) are also reported here. All complexes 1–4 are characterized by several physicochemical techniques and the structural features of 1 and 2 have been solved by X‐ray crystallography. The proposed mechanism of molybdenum‐mediated interligand C–C bond formation is supported by DFT calculations including the comparisons with the synthesized vanadium analogues. The catalytic potentials of 1–4 for the epoxidation of styrene and cyclohexene have also been explored.