Janus nanoparticles could exhibit a higher interfacial activity and adsorb stronger to fluid interfaces than homogeneous nanoparticles of similar sizes. However, little is known about the interfacial diffusion of Janus nanoparticles and how it compares to that of homogeneous ones. Here, we employed fluorescence correlation spectroscopy to study the lateral diffusion of ligand-grafted Janus nanoparticles adsorbed at water/oil interfaces. We found that the diffusion was significantly slower than that of homogeneous nanoparticles. We carried out dissipative particle dynamic simulations to study the mechanism of interfacial slowdown. Good agreement between experimental and simulation results has been only obtained provided that the flexibility of ligands grafted on the nanoparticle surface was taken into account. The polymeric ligands were deformed and oriented at an interface so that the effective radius of Janus nanoparticles is larger than the nominal one obtained by measuring the diffusion in bulk solution. These findings highlight further the critical importance of the ligands grafted on Janus nanoparticles for applications involving nanoparticle adsorption at an interface, such as oil recovery or two-dimensional self-assembly.