Silicon photonics have attracted significant interest because of their potential in integrated photonics components and all-dielectric meta-optics elements. One major challenge is to achieve active control via strong photon-photon interactions, i.e. optical nonlinearity, which is intrinsically weak in silicon. To boost the nonlinear response, practical applications rely on resonant structures such as microring resonators or photonic crystals. Nevertheless, their typical footprints are larger than 10 μm. Here, we show that 100 nm silicon nano-resonators exhibit a giant photothermal nonlinearity, yielding 90% reversible and repeatable modulation from linear scattering response at low excitation intensities. The equivalent nonlinear index is five-orders larger compared with bulk, based on Mie resonance enhanced absorption and high-efficiency heating in thermally isolated nanostructures. Furthermore, the nanoscale thermal relaxation time reaches nanosecond. This large and fast nonlinearity leads to potential applications for GHz all-optical control at the nanoscale and super-resolution imaging of silicon.