Controlled and simple synthesis strategy of two-dimensional (2D) nanomaterials is critical for designing the related heterostructures with different geometries, which influence strain, electronic structures, light-interactions, and surface reactions. Here, we report a single-step growth method for wrinkled MoSe2 thin films on flat SiO2/Si substrates by using high-vacuum co-evaporation. Above the critical film thickness of 15-20 nm, the MoSe2 films start to form wrinkled structure with lateral periodicity of 7-10 mu m, which significantly reduces light reflectance in the visible range. We demonstrate formation of the wrinkled pattern on the selective area either by etching the substrate surface or by depositing gold films. In addition, we observe switching of the microscopic growth mode from a layered stacking to a vertically aligned growth, which results in 2D-3D hybrid microstructures. Our single-step synthesis approach might be generalized to obtain wrinkled 2D-3D hybrid nanomaterials and utilized for flexible electronic & optoelectronic devices, efficient solar cells, catalytic electrodes, and anti-counterfeiting applications.