Since quasi-phase-matching of nonlinear optics was proposed in 1962, nonlinear photonic crystals were rapidly developed by ferroelectric domain inversion induced by electric or light poling. The three-dimensional (3D) periodical rotation of ferroelectric domains may add feasible modulation to the nonlinear coefficients and break the rigid requirements for the incident light and polarization direction in traditional quasi-phase-matching media. However, 3D rotating ferroelectric domains are difficult to fabricate by the direct external poling technique. Here, we show a natural potassium–tantalate–niobate (KTN) perovskite nonlinear photonic crystal with spontaneous Rubik's cube-like domain structures near the Curie temperature of 40 °C. The KTN crystal contains 3D ferroelectric polarization distributions corresponding to the reconfigured second-order susceptibilities, which can provide rich reciprocal vectors to compensate for the phase mismatch along an arbitrary direction and polarization of incident light. Bragg diffraction and broadband second-harmonic generation are also presented. This natural nonlinear photonic crystal directly meets the 3D quasi-phase-matching condition without external poling and establishes a promising platform for all-optical nonlinear beam shaping and enables new optoelectronic applications for perovskite ferroelectrics.