This Letter introduces a CMOS depth sensor with a multi-resolution single-photon avalanche diode (SPAD) array and area-efficient filter circuit with a programmable reference for environment-adaptive noise suppression. Four SPADs compose a macro-pixel for detecting targets at a short distance with high resolution, whereas 4 × 4 SPADs are reconfigured to a super-pixel for a long distance with enhanced signal-to-noise ratio. To provide environment-adaptive noise suppression in the miniaturised SPAD array, an area-efficient filter circuit with a programmable reference is proposed: a digital macro-filter corresponding to a macro-pixel and an analogue super filter corresponding to a super-pixel. The prototype chip was fabricated with a 110 nm CMOS image-sensor process, including 128 SPAD farm arrays and 128 analogue front-end circuits. With high background light of over 90 klx and a high dark-count rate of over 27.1 kHz, the time-of-flight could be measured by filtering out invalid pulses from noise without using multiple time-to-digital converters per pixel, which enables the implementation of miniaturised LiDAR-sensor systems on a chip.