In this study, a new fluorescence sensor M1 consisting of 4,4-difluoro-4-bora-3a,4a-diazaindacene (BODIPY) and thiosemicarbazide moieties was designed for mercury ion detection. M1 exhibited intense green emission in both solution and solid state. Obvious fluorescence quenching of the solution of M1 in DMF/H2O was observed only in presence of Hg2+ among the metal ions (Hg2+, Li+, Co2+, Cr3+, Mg2+, K+, Mn2+, Al3+, Fe3+, Zn2+, Cu2+, Cd2+, Ag+, Pb2+, Ca2+, Ni2+, Ba2+). The present probe M1 was 1:1 complexed with mercury ion, with complexation constant of 2.98 × 104 M−1. The detection limit of the probe M1 was calculated to be as low as 4.9 × 10−7 M. Moreover, the probe M1 achieved selective and sensitive sensing toward mercury ion on test strips, which guaranteed its potential application.