Alendronic acid modified resol nanocomposite resins (AA‐PFNCRs) and sepiolite modified resol nanocomposite resins (SEP‐PFNCRs) have been synthesized by in situ method in the presence of base catalyst. Additionally, the synergistic effects of alendronic acid and sepiolite clay (AA‐SEP‐PFNCR) on the resol resin have been studied. The structure, morphology, and thermal properties of these nanocomposites have been investigated by Fourier Transform Infrared Spectroscopy (FTIR), Differential Scanning Calorimetry (DSC), Thermogravimetric Analysis (TGA), and X‐ray Diffraction (XRD). The results demonstrated the interactions between the fillers and resol resin. Thermal properties of nanocomposite resins were improved due to alendronic acid and sepiolite. The obtained samples were also characterized morphologically by Scanning Electron Microscope (SEM). © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43807.