The Three-Dimensional (3-D) Otsu’s method is an effective improvement on the traditional Otsu’s method. However, it not only has high computational complexity, but also needs to improve its anti-noise ability. This paper presents a new Otsu’s method based on 3-D histogram. This method transforms 3-D histogram into a 1-D histogram by a plane that is perpendicular to the main diagonal of the 3-D histogram, and designs a new maximum variance criterion for threshold selection. In order to enhance its anti-noise ability, a method based on geometric analysis, which can correct noise, is used for image segmentation. Simulation experiments show that this method has stronger anti-noise ability and less time consumption, comparing with the conventional 3-D Otsu’s method, the recursive 3-D Otsu’s method, the 3-D Otsu’s method with SFLA, the equivalent 3-D Otsu’s method and the improved 3-D Otsu’s method