Se and MoSe2 nanoflakes are prepared in N2 environment by hot filament chemical vapor deposition through using Se and MoO3 powders as the source materials. The structures and compositions of Se and MoSe2 nanoflakes are systemically studied by using field emission scanning electron microscope, transmission electron microscope, energy dispersive X-ray spectroscope, micro-Raman spectroscope, and X-ray photoelectron spectroscope. The results indicate that the mixing of the Se and MoO3 powders directly affects the formations and structures of Se and MoSe2 nanoflakes. When the Se and MoO3 powders are fully mixed, the Se nanoflakes are formed, however the MoSe2 nanoflakes are formed under no mixture of Se and MoO3 powders. This is due to the fact that different reactions of Se and MoO3 powders in gas environment with or without mixing the Se and MoO3 powders are generated. The study of photoluminescence properties indicates that the photoluminescence peaks are generated at about 774, 783 nm and 783, 784 nm for the Se and MoSe2 nanoflakes, respectively, which are different from the photoluminescence properties of monolayer MoSe2 nanosheet. These outcomes can enrich our knowledge of the synthesis and optical properties of two-dimensional Se-based nanomaterials and will contribute to the development of optoelectronic devices of two-dimensional Se-based nanomaterials.