In this study, a novel nanostructure of amorphous MoSex was produced by a facile low-temperature hydrothermal method. Better adsorption and photodegradation of rhodamine B (RhB) and methylene blue (MB) were achieved with amorphous MoSex than with crystalline MoSex under dark conditions and visible light irradiation. More importantly, the catalytic mechanisms of the amorphous and crystalline samples were compared by free radical-trapping experiments. The results showed that the main active substance that increased the photocatalytic activity in amorphous MoSex was superoxide radicals (O-center dot(2)-), whereas the main active substances for crystalline MoSex were holes (h(+)) and hydroxyl radicals ((OH)-O-center dot). In addition, amorphous MoSex had more unsaturated atoms and a greater specific surface area because of its unique amorphous structure, thus enhancing its photocatalytic performance and adsorption capacity. The study of amorphous molybdenum selenide provides a new idea for improving the photocatalytic activity of two-dimensional materials, which is of great significance.