Influenza is a major respiratory infection associated with significant morbidity in the general population and mortality in elderly and high-risk patients. It is an RNA virus that contains two major surface glycoproteins, neuraminidase and hemagglutinin. These proteins are essential for infection. Neuraminidase has been found to be a potential target to control influenza virus. Here, we have developed three-dimensional holographic vector of atomic interaction field analysis as a new method of quantitative structure-activity relationships for different sets of compounds to understand chemical-biological interactions governing their activities toward influenza neuraminidase. Good results, R = 0.885, SD = 0.848, R(CV) = 0.858 (the maximum) and SD(CV) = 0.934 (the minimum), showed that holographic vector of atomic interaction field analysis can be applicable to molecular structural characterization and biological activity prediction and quantitative structure-activity relationship model had favorable stability and prediction capability.