Abstract: Optimizations of the geometry structure of quercetin were performed using DFT/B3LYP with five basis sets,HF with three basis sets and semi-empirical method AM1.Then a comparison among the calculated and the experimental results from the determination of crystal structures was done.Several advices have been given that are related with the geometry optimization of the organic molecules which have non-planar and conjugated structure,based on the analysis of the differences between the optimized and the experimental geometries,the relationship and the contrast of minimum energies between basis sets and the optimized results.