Facile synthesis of nano porous organic cages with small size and good fluorescence property is highly desirable, but still challenging and scarce for their sensing applications. Here we report a rapid room-temperature recrystallization method for the preparation of nano porous organic cages with ultra-small size as a fluorescent probe for copper ion. The prepared nano porous organic cages gave the diameter of 2.49 ± 0.04 nm, and exhibited stable emission at 535 nm with absolute quantum yield of 0.68%. On the basis of the coordination interaction and charge transfer between the nano porous organic cages and copper ion, a simple fluorescent probe for copper ion in aqueous solution was developed. The developed method gave a calibration function of QE = 0.4815lg[Cu2+] + 0.5847 (where QE is the quenching efficiency; [Cu2+] in μM) (R2 = 0.9987) in a concentration range of 0.1–2 μM, the limit of detection (3s) of 8 nM, and the relative standard deviation of 0.36% for 10 replicate determinations of 0.5 μM copper ion. The recoveries of spiked copper ion in tap water samples ranged from 96.8% to 103.0%. The proposed method possesses good sensitivity, selectivity and accuracy.