Single photons constitute a main platform in quantum science and technology: they carry quantum information over extended distances in the future quantum internet and can be manipulated in advanced photonic circuits enabling scalable photonic quantum computing. The main challenge in quantum photonics is how to generate advanced entangled resource states and efficient light-matter interfaces. Here we utilize the efficient and coherent coupling of a single quantum emitter to a nanophotonic waveguide for realizing quantum nonlinear interaction between single-photon wavepackets. This inherently multimode quantum system constitutes a new research frontier in quantum optics. We demonstrate control of a photon with another photon and experimentally unravel the dynamical response of two-photon interactions mediated by a quantum emitter, and show that the induced quantum correlations are controlled by the pulse duration. The work will open new avenues for tailoring complex photonic quantum resource states.