For the features of the optical transmission in photonic crystal fiber the minimum roots of mean square search method was proposed. The minimum root-mean -square search method was used to estimate the deviation between the theory of the Localized Basis Functions Method and experimental result of optical transmission in photonic crystal fiber. The experimental result was the light intensity distribution in the end of the photonic crystal fiber. The process of estimation deviation had five steps. The first one was to found the corresponding equivalency light intensity curves for the experimental result and the theory of the Localized Basis Functions Method. The second one was to normalize the corresponding equivalency light intensity curves with equivalency distances. The distance was the mean distance between the all points in the curve and the centre. The third one was to found the minimum distance between the point in the experimental curve and the all points in corresponding theoretical curve. The fourth one was that the root of mean square for the minimum distances of the feature points in experimental curve was calculated. The fifth one was that the roots of mean square for the all experimental curves were obtained. The deviations of the equivalency light intensity curves compared to the theoretical results were 4%, 3%, 3%, 3%, and 8%, respectively. The second curve was omitted from outer to inner in experimental curves. The results were shown that the minimum root-mean-square search method was a good method for estimating the deviation between the theory of the Localized Basis Functions Method and experimental result of optical transmission in photonic crystal fiber.
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