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Inverse design is a powerful tool in wave physics for compact, high-performance devices. To date, applications in photonics have mostly been limited to linear systems and it has rarely been investigated or demonstrated in the nonlinear regime. In addition, the “black box” nature of inverse design techniques has hindered the understanding of optimized inverse-designed structures. We propose an inverse design method with interpretable results to enhance the efficiency of on-chip photon generation rate through nonlinear processes by controlling the effective phase-matching conditions. We fabricate and characterize a compact, inverse-designed device using a silicon-on-insulator platform that allows a spontaneous four-wave mixing process to generate photon pairs at a rate of 1.1 MHz with a coincidence to accidental ratio of 162. Our design method accounts for fabrication constraints and can be used for scalable quantum light sources in large-scale communication and computing applications.