Toxicities (–lgEC50) of 16 halogeno-benzenes against vibrio qinghaiensis (Q67) were measured systematically, and their 2D-QSAR model (R2= 0.875, q2= 0.821) was established, which included two parameters: averaged polarizability (α) and total energy (TE). The proposed model indicated that the toxicities of this kind of compounds were proportionate to α, i.e., their toxicities were relative to the molecular volume. Furthermore, 3D-QSAR model (R2 = 0.929, q2 = 0.712) of –lgEC50 was proposed by using comparative molecular force field (CoMFA) based on the molecular simulation. To our interest, 3D-QSAR model suggested that the hydrophobicity of substituents was the dominating factor for the toxicities, the electrostatic effect was the secondly important, and the steric field gave the least contribution. Comparably, the prediction ability of the 3D-QSAR model is slightly more advantageous than that of 2D-QSAR, and they can be used complementally in the toxicity description of this kind of compounds.