As an important regulatory method, the phase engineering strategy is widely used to develop functional materials with desired properties. Herein, we combine a solvothermal method with post-annealing treatment to controllably synthesize multifunctional MoSe flower-like nanostructures (FNSs) in different crystal phases. Based on the different phases of MoSe FNSs, we systematically investigate their performance in lithium-ion storage, the hydrogen evolution reaction (HER), and the hydrogenation of nitrophenol. The results show that 1T-MoSe FNSs possess superior performance in lithium-ion batteries, HER, and hydrogenation of PNP compared with 2H-MoSe FNSs. Moreover, density functional theory calculations reveal that 1T-MoSe FNSs exhibits a higher chemisorption energy than that of 2H-MoSe FNSs, which is beneficial for the improvement of the lithium-ion storage capacity. This work provides an effective way to develop functional materials based on phase engineering.