The productions of multiply charged ions in the interactions of intense nanosecond laser pulse with clusters have aroused broad interests in molecular physics. Benzene, cyclohexene and cyclohexane clusters are chosen to study the effect of multiphoton ionization (MPI) efficiency on the relative intensity of multiply charged ions, as they possess similar molecular structures and the same element constitutions. They are ionized with a 5 ns Nd-YAG nanosecond laser. The carbon charge state produced by cyclohexene and cyclohexane is about 4; while by benzene is only about 3. The ratios of C3+/C2+ for cyclohexane, cyclohexene and benzene are 1.1, 0.6 and 0.4, respectively. The relative MPI efficiencies of three molecules are measured to be in the magnitude sequence of benzene > cyclohexene > cyclohenane by diffusion beam. Higher MPI efficiency of molecules can cause more than one molecules to be ionized at the edge of laser pulse, the Coulomb repelling force between adjacent ions leads clusters to early split into small size ones, which will prevent the production of the highly charged ions.