Interfacial polarization and geometrical morphology play a significant role in the attenuation of electromagnetic (EM) wave. Herein, the two-dimensional (2D)/2D heterojunction with flower-like geometrical morphology is proposed and produced, which may simultaneously provide a large contact area for achieving strong interfacial polarization and activates more sites for the possible multiple EM wave reflection and scattering. By adopting a simple two-step hydrothermal method, MoSe₂/MoS₂and MoS₂/MoSe₂ inner and outer-interchangeable heterojunctions consisting of 2D MoSe₂ and MoS₂ nanosheets with flower-like geometrical morphology were successfully synthesized. The results revealed that the hydrothermal temperatures significantly impacted the flower-like geometrical morphology and MoS₂ content. By optimizing the microstructures, the designed MoSe₂/MoS₂ and MoS₂/MoSe₂ heterojunctions presented enhanced comprehensive EM wave absorption properties (EMWAPs), possessing strong absorption capability, wide absorption bandwidth and thin matching thicknesses. Generally, this work demonstrates that the optimized EMWAPs of designed heterojunctions mainly originate from the special interfaces and morphology configuration, which also paves a new way for the designing and synthesis of transition metal dichalcogenides-based heterojunction as a novel and desirable candidate for high-performance microwave absorbers.