The deposition defects, known as a transition from Y- to X-type deposition, during the Langmuir-Blodgett (LB) film deposition were analyzed by the measurement of the reflectivity of small angle X-rays using synchrotron radiation. The reflectivity profile of the cadmium arachidate LB film over a wide range of grazing angles was obtained. By fitting the location and dispersion of the subsidiary maxima between the Bragg peaks of the experimentally measured reflectivity profile with that of the calculated reflectivity profile, the average thickness and the distribution of layer thickness were evaluated. A Monte Carlo simulation was performed for the transition of Y- to X-type deposition by using a probability of surface molecule detachment accounting between neighboring molecules. The genetic algorithm was incorporated into Monte Carlo simulation to get the optimum value of the probability factors. The distribution of layers having different thickness predicted by the simulation correlates well with that obtained from the X-ray reflectivity analysis. Based on the morphology measurement with an atomic force microscopy (AFM), the domain structure and mean roughness of LB films were obtained. The mean roughness value calculated based on the number of layer distribution is consistent with that obtained from X-ray reflectivity analysis.