Using the Gaussian 03 program, the thermodynamic properties of 76 polychlorinated anthraquinones (PCAQNS) have been calculated by density functional theory (DFT) at the BHandHLYP/6-311G** level. On the basis of the output data of Gaussian, the isodesmic reactions are designed to calculate the standard enthalpy of formation and standard Gibbs energy of formation of PCAQN congeners. The relations of these thermodynamic parameters with the number and position of Cl atom substitution (N(PCS)) are discussed, and the order of relative stability of PCAQN congeners is theoretically proposed according to the relative magnitude of their standard Gibbs energy of formation. The results were also compared with those of polychlorinated dibenzo-p-dioxins (PCDDs). In addition, the values of molar heat capacities at constant pressure (C(p,m)) from (200 to 1000) K for PCAQN congeners are calculated, and the temperature dependence relation of this parameter is obtained using the least-squares method. Finally, the toxicity orders of PCAQNs were predicted according to previous experience.