Fates of toxic foundational groups of Microcystin-LR in aqueous have garnered widespread attention because of the difficulty of removal during photocatalytic process. Here, an efficient N, P co-doped TiO₂/expanded graphite (NPTEG) floating material (NPTEG) modified by poly dimethyl diallyl ammonium chloride (PDDA) and graphitic carbon nitride (g-C₃N₄) (x PDDA-g-C₃N₄-NPTEG) was assembled and used to destroy the toxic foundational groups of MC-LR in water. g-C₃N₄ can match well with TiO₂ to form heterojunction where holes can gather in the valence band of g-C₃N₄. PDDA is used to passivate the g-C₃N₄, and performs as holes transport layer during the photocatalytic process to promote the separation of electron-hole pairs. Under the direct interaction of photo-generated holes and free carboxyl groups of MC-LR adsorbed on the surface, the decarboxylation process in the free acid groups on D-glutamic acid (Glu) and methyl-D-aspartic acid (D-MeAsp) of MC-LR occurred which was authenticated by UPLC-ESI-MS/MS. Meanwhile, the conjugated double bond was also removed by hydroxylation, so as to achieve the goal of non-toxic site residues in the degradation process. Furthermore, the degradation byproducts toxicity and photocatalysts stability were explored. The results confirm that x PDDA-g-C₃N₄-NPTEG exhibits excellent attacking ability of carboxylic acid groups of MC-LR and high recycle ability, which has great promise as a means of effectively treating drinking water.