Owing to its thickness-modulated direct energy band gap, relatively strong light–matter interaction, and unique nonlinear optical response at a long wavelength, few-layer black phosphorus, or phosphorene, becomes very attractive in ultrafast photonics applications. Herein, we synthesized a graphene/phosphorene nano-heterojunction using a liquid phase-stripping method. Tiny lattice distortions in graphene and phosphorene suggest the formation of a nano-heterojunction between graphene and phosphorene nanosheets. In addition, we systematically investigate their nonlinear optical responses at different wavelength regimes. Our experiments indicate that the combined advantages of ultrafast relaxation, broadband response in graphene, and the strong light–matter interaction in phosphorene can be combined together by nano-heterojunction. We have further fabricated two-dimensional (2D) nano-heterojunction based optical saturable absorbers and integrated them into an erbium-doped fiber laser to demonstrate the generation of a stable ultrashort pulse down to 148 fs. Our results indicate that a graphene/phosphorene nano-heterojunction can operate as a promising saturable absorber for ultrafast laser systems with ultrahigh pulse energy and ultranarrow pulse duration. We believe this work opens up a new approach to designing 2D heterointerfaces for applications in ultrafast photonics and other research. The fabrication of a 2D nano-heterojunction assembled from stacking different 2D materials, via this facile and scalable growth approach, paves the way for the formation and tuning of new 2D materials with desirable photonic properties and applications.