Silicon photonics has been developed successfully with a top-down fabrication technique to enable large-scale photonic integrated circuits with high reproducibility, but is limited intrinsically by the material capability for active or nonlinear applications. On the other hand, free-standing nanowires synthesized via a bottom-up growth present great material diversity and structural uniformity, but precisely assembling free-standing nanowires for on-demand photonic functionality remains a great challenge. Here we report hybrid integration of free-standing nanowires into silicon photonics with high flexibility by coupling free-standing nanowires onto target silicon waveguides that are simultaneously used for precise positioning. Coupling efficiency between a free-standing nanowire and a silicon waveguide is up to ~97% in the telecommunication band. A hybrid nonlinear-free-standing nanowires–silicon waveguides Mach–Zehnder interferometer and a racetrack resonator for significantly enhanced optical modulation are experimentally demonstrated, as well as hybrid active-free-standing nanowires–silicon waveguides circuits for light generation. These results suggest an alternative approach to flexible multifunctional on-chip nanophotonic devices.