MoSe2 is a compelling narrow-band-gap semiconductor with particular lamellar crystal structure, but which is rarely used as microwave absorber filler. Owing to the analogue molecular structure with MoS2, it may be a potential dielectric dissipation candidate. The hierarchical flower-like structure has been wide accepted as attractive morphology due to its possible strong multiple scattering and reflecting abilities for microwave, thus, in this study, we employed a facile solvothermal process to fabricate the unique flower-like MoSe2 spheres for eliminating microwave interference issue. Further through the precise tuning of morphology configurations of flower-like MoSe2, the effective absorption to specific microwave frequency band can be well optimized, even including low-frequency band. The microwave absorption (MA) performance results show that the dense-flower samples could achieve full absorption in Ku-band and blooming-flower samples cover the entire X-band. The hollow-flower sample is good at absorption in low frequency of C-band and X-band. Our work not only develops outstanding microwave absorber candidates through delicate nanostructure design, but also paves a new way for tuning effective frequency band via tailoring morphology configurations.