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In this work, a single photon avalanche diode (SPAD) based configurable photon counting system is developed. The photon counting system is able to operate in three working modes to enhance the system's different performance characteristics for various use cases (e.g., strong/weak incident light signal, high/low ambient light, long/short distance ranging/sensing). The working modes can be switched digitally by the user or signal processing circuit that makes it possible to add intelligent control logic for switching in real-time between working modes to achieve a stable and optimized performance when it is used under varying working conditions. Performance characteristics of the system operation in each working mode are measured and compared.