Study on the quantitative structure-activity relationship (QSAR) of 26 compounds, N-[5-(2-furanyl)-2-methyl-4-oxo-4H-thieno[2,3-d]pyrimidin-3-yl]-carboxamide and 3-substituted-5-(2-furanyl)-2-methyl-3H-thieno[2,3-d]pyrimidin-4-ones, with three-dimensional holographic vector of atomic interaction field (3D-HoVAIF) was carried out. SMR-PLS QSAR models have been created and good correlation coefficients and cross-validated correlation coefficients were obtained. The result shows that the models have good prediction capability and favorable stability and the 3D-HoVAIF is applicable to the molecular structural characterization and biological activity prediction. Study on the quantitative structure-activity relationship (QSAR) of 26 compounds, N- [5- (2-furanyl) -2-methyl- 4- oxo-4H-thieno [2,3- d] pyrimidin-3-yl] -carboxamide and 3-substituted-5- (2-furanyl) -2-methyl-3H-thieno [2,3- d] pyrimidin-4-ones with three- dimensional holographic vector of atomic interaction field (3D- HoVAIF) was carried out. SMR-PLS QSAR models have been created and good correlation coefficients and cross-validated correlation coefficients were obtained. The result shows that the models have good prediction capability and favorable stability and the 3D-HoVAIF is applicable to the molecular structural characterization and biological activity prediction.