Molybdenum disulfide (MoS2) is a notable two-dimensional (2D) transition metal dichalcogenide (TMD) with properties ideal for nanoelectronic and optoelectronic applications. With growing interest in the material, it is critical to understand its layer-number-dependent properties and develop strategies for controlling them. Here, we demonstrate a photo-modulation of MoS2 flakes and elucidate layer-number-dependent charge transfer behaviors. We fabricated hybrid structures by functionalizing MoS2 flakes with a uniform layer of photochromic diarylethene (DAE) molecules that can switch between closed- and open-form isomers under UV and visible light, respectively. We discovered that the closed-form DAE quenches the photoluminescence (PL) of monolayer MoS2 when excited at 633 nm and that the PL fully recovers after DAE isomerization into the open-form. Similarly, the electric conductivity of monolayer MoS2 is drastically enhanced when interacting with the closed-form isomers. In contrast, photoinduced isomerization did not modulate the properties of the hybrids made of MoS2 bilayers and trilayers. Density functional theory (DFT) calculations revealed that a hole transfer from monolayer MoS2 to the closed-form isomer took place due to energy level alignments, but such interactions were prohibited with open-form DAE. Computational results also indicated negligible charge transfer at the hybrid interfaces with bilayer and trilayer MoS2. These findings highlight the critical role of layer-number-dependent interactions in MoS2-DAE hybrids, offering valuable insights for the development of advanced photoswitchable devices.