Paraquat is a highly toxic cationic agrochemical, and distinguishing it from other electron-deficient species is still a pending issue via fluorescence detection. In this work, taking advantage of the structural similarity, pyrene-based MOFs were applied in the analysis of paraquat in both aqueous and organic phases, and an anionic ligand was further introduced into the structures of MOF precursors in the hope of using electrostatic attraction to improve the sensing performance. Experimental observation showed that the backbone structure of the MOF has a profound effect on the response sensitivity, and the improvement by the anionic ligand depends heavily on the medium of the analysis. An anionic ligand installed derivative was screened for the detection of paraquat in the organic phase. The recognition of paraquat from a series of electron deficient agrochemicals and nM-scale detection limits were achieved in this system.