In this paper we present a novel method to visualize weather data with multi-layer controllable texture synthesis. Texture possesses multiple principal perceptual channels, which makes it good at encoding multiple data attributes contained in weather data. The natural textures existed in the real world especially provide plenty of choices to encode the data with visually pleasing images. A controllable texture synthesis method is developed to generate a large amount of textures which change the appearances of their individual perceptual dimensions according to the underlying distribution of data attributes. In order to encode more data attributes we further propose multi-layer texture synthesis. The background and foreground textures are separately synthesized and then combined together for display. In the end, we apply our method to some real-world weather data and demonstrate its effectiveness with a user study.