In this article, isothermal crystallization kinetic of the linear hydroxyl polyester urethane (PUR), as well as influence of amorphous silica nanofiller, was investigated. With the aim to investigate the influence of filler surface modification on the crystallization process of polyurethane matrix, nonmodified silica, as well as silica modified with methacrylsilane and octylsilane, were used as fillers for PUR composite preparation. The crystallization kinetics depending on temperature of the isothermal crystallization and volume fraction of filler by using differential scanning calorimetry (DSC) were investigated. The measurements at temperatures 7, 12, and 17°C for PUR and composites with 0.5, 1, 2, and 4 vol % of filler were done. Kinetic parameters of the isothermal crystallization n and K were determined according to Avrami model. Melting of the isothermally crystallized samples was also investigated. Results of the research indicate that by increasing the isothermal crystallization temperature, the crystallization rate of the PUR soft phase decreases and that the perfection of the crystallites is improved. By addition of all fillers up to ≈1 vol %, the crystallization rate increases; however, addition of a higher amount of the filler significantly decreases the crystallization rate. It was found that surface modification can significantly affect crystallization rate and that the nucleation efficiency of silica increases in the following order: methacrylsilane‐modified silica < nonmodified silica < octylsilane‐modified silica. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013