Nanoporous TiO2 thin films are deposited directly onto substrates by a one-step stagnation flame synthesis with organometallic precursors. The deposition mechanism in the stagnation-point boundary layer is intensively studied. For the first time, the radial profile of nanoparticle deposition flux is measured using a novel method of concentric collecting rings, which exhibits similar trend with the heat flux profile of stagnation-point flows. Then, we develop the mathematical model of nanoparticle transport and deposition in the stagnation-point boundary layer for further clarifying experimental results, especially the effects of substrate temperatures and in-situ produced particle sizes. Both thermophoresis in an inner part of boundary layer and thermal compression/expansion of the gas phase are found to play important roles in determining the deposition flux. The contribution of Brownian diffusion, determined by a thermophoretic Peclet number, is inappreciable compared to thermophoresis until particle diameter is as small as 2 nm. The results in this work support a conclusion of size-independence of the thermophoretic velocity, implying that the rigid-body collision assumption of Waldmann’s formula is not accurate for small particles especially less than 10 nm. This study can be generally applied to other deposition techniques of thin films.