Traditional analytical methods of thorium contamination suffer from several disadvantages such as time-consuming procedures and an equipment-intensive nature, leading to substantial challenges in rapid and on-site monitoring of thorium concentrations in complex natural water systems. We report here the first case of a luminescent metal organic framework based probe (ThP-1) for highly sensitive and selective self-calibrated sensing of Th4+ contamination in natural fresh water media with a notably facilitated detection procedure. The detection limit of ThP-1 was determined to be 24.2 μg/L, much lower than the thorium contamination standard of 246 μg/L in drinking water defined by the World Health Organization. Importantly, the detection procedure based on the rarely reported self-calibration manner is greatly beneficial in improving the detection accuracy. The self-calibrated luminescence evolution process shows a great anti-interference ability capable of detecting thorium contamination in a wide concentration range from 24.2 μg/L to 300 mg/L, which can not be achieved directly by the traditional methods. The Th4+-selective luminescence response originates from the selective uptake and efficient enrichment of Th4+ by the host framework of ThP-1 through inner-sphere coordination, which is further confirmed by batch experiments, X-ray absorption spectroscopic study, and DFT calculations.