• The customized flower-like Co-based heterostructures (CoO/MCo 2 O 4 , M=Fe, Cu, Zn) were successfully synthesis through identical hydrothermal route. • The introduction of different metal ions enables to modulate the components, heterogeneous interfaces and defects for tailoring the electromagnetic parameters. • The permittivity decreases gradually in the order of Fe 2+ , Cu 2+ , Zn 2+ , making it possible to tune absorption peak position and frequency band. • When filler content is 10 wt%, the CoO/CuCo 2 O 4 possesses RL min of –52.67 dB and corresponding EAB of 4.48 GHz at 1.90 mm. Lightweight and high-efficiency absorbing materials equipped with tunable electromagnetic properties are the foremost important factors for driving applications of 5G smart era and military stealth. Stimulated by the remarkable merits of heterogeneous interface engineering, a series of unique flower-like Co-based multiphases nanostructures were successfully synthesized through identical hydrothermal method, and subsequently anchored on the Ti 3 C 2 T x nanosheets. The suitable metal ion modulation is feasible to regulate the components, heterogeneous interfaces and defects for tailoring the electromagnetic parameters and microwave absorption (MA) property. Notably, the permittivity decreases of CMOT (CoO/MCo 2 O 4 /Ti 3 C 2 T x , M=Fe, Cu, Zn) composites proceed gradually in the order of Fe 2+ , Cu 2+ , Zn 2+ , while the MA performance with tunable absorption peak could be modulated subtly. The as-obtained CFOT-12 (10 wt%), CCOT-15(10 wt%) and CZOT-15 (15 wt%) exhibit excellent MA capacity with a minimum reflection loss (RL min ) of –41.06, –52.67, –52.52 dB and corresponding effective absorption bandwidth (EAB) of 3.68, 4.48, 3.92 GHz at 2.10, 1.90, 1.80 mm, respectively. This work expands a novel approach to construct multicomponent heterostructure for tuning the EM parameters and absorbing property, as well as realize the high efficient and light weight.