Isomers based on the RS and EZ geometrical isomerism of the neutral, deprotonated species of HMPAO and their complexes with zinc(Ⅱ) ion have been investigated by semiempirical AM1 optimization method. The Hartree-Fock energies on AM1 geometries o f HMPAO species were calculated with HF/6-31G* methods. Twenty-two isomers of the neutral and twenty isomers of the deprotonated species of HMPAO have been found. The presence of four EE-series isomers of both zinc(Ⅱ) complexes with the neutral and deprotonated HMPAO have been expected and the SREE typical isomer of both types of complexes is the most stable isomer. Energies of complexation of zinc(Ⅱ)/HMPAO isomers with AM1 geometries were calculated by HF/ 6-31G*method. Due to the complexations with zinc(Ⅱ), the structural reorganizations of some isomers of the neutral HMPAO have been occurred. The optimized geometrical parameters of the related conformations have been discussed in terms of their stabilities and existences.