Effects of the deposition process parameters on the thickness of TiO2 nanostructured film were simulated using the molecular dynamics (MD) approach and modeled by the artificial neural network (ANN) and regression method. Accordingly, TiO2 nanostructured film was prepared experimentally with the sol–gel dip‐coating method. Structural instabilities can be expected, due to short‐ and/or long‐range intermolecular forces, leading to the surface inhomogeneities. In the MD simulation, the Morse potential function was used for the inter‐atomic interactions, and equations of motion for atoms were solved by Verlet algorithm. The effect of the withdrawal velocity, drying temperature and number of deposited layers were studied in order to characterize the film thickness. The results of MD simulations are reasonably consistent with atomic force microscopy, scanning electron microscopy and Dektak surface profiler. Finally, the outputs from experimental data were analyzed by using the ANN in order to investigate the effects of deposition process parameters on the film thickness. In this case, various architectures have been checked using 75% of experimental data for training of the ANN. Among the various architectures, feed‐forward back‐propagation network with trainer training algorithm was found as the best architecture. Based on the R‐squared value, the ANN is better than the regression model in predicting the film thickness. The statistical analysis for those results was then used to verify the fitness of the complex process model. Based on the results, this modeling methodology can explain the characteristics of the TiO2 nanostructured thin film and growth mechanism varying with process conditions. © 2013 The Authors. Surface and Interface Analysis published by John Wiley & Sons Ltd.