Polyoxometalate (POM) clusters containing lanthanide ion (LnPOM) possess excellent luminescence features, but the envisaged applications are hindered by the challenges in integration into functional architectures. Herein, a novel cross-linked cyclodextrin (CL-CD) and LnPOM composite is developed and applied for discriminative detection of inorganic and organic phosphate phases. For inorganic phosphates, a ratiometric fluorescence response is demonstrated with excellent selectivity, and anti-interference ability in complex analyte mixtures. The outstanding performance is attributed to the high affinity of POM and distinct interactions between La3+ and Eu3+ with the phosphate. For organophosphates, a “signal-off” fluorescence response for p-nitrophenyl-substituted organophosphates is discovered due to the encapsulation of nitrophenyl group into the hydrophobic cavity of CD that enhances the interactions between POM and p-nitrophenyl phosphate. The discriminative responses of CL-CD–LnPOM to inorganic phosphates and organophosphates bring new insights into POM-based fluorescence probes for the detection of inorganic and organic phases based on the intrinsic structural difference between the phosphate analogs.