Due to the rise of microbial strains resistant to conventional therapies, there is an urgent need for finding the new antimicrobial chemotypes. Heterocyclic compounds such as thiocarbohydrazones (TCHs) are able to interact with many metalloenzymes essential for microbes, while sulfur atom increases lipophilicity which is generally positively correlated with potency. In this paper, we report antibacterial and antifungal activity of twenty-two TCHs toward eight bacterial and three fungal strains. Furthermore, three alignment independent 3D QSAR models based on descriptors derived from molecular interaction fields (MIFs) are developed in order to rationalize structure-activity relationships for activities of TCHs toward S. aureus, P. aeruginosa and C. albicans. Several structural fragments important for biological activity are recognized in each model, and structural modifications which could lead to increased potency are suggested. Designed structures will be synthesized accordingly and tested toward the same microbial strains in order to obtain more potent derivatives.