Based on the obvious anisotropy of Xisha Islands waters topography, the uneven fractal characteristics of Xisha Islands waters topography are studied by using multivariate linear expression. Using multiple linear regression analysis method to extract the projection of heterogeneous characteristic factors, the geometric heterogeneous characteristics of Xisha Islands waters are obtained. The fractal feature of landform is studied based on projection coverage method, and the non-isotropic body irregularity in Xisha Islands waters is measured. Experimental results show that this method can effectively analyze the non-uniform fractal characteristics of the Xisha Islands waters. The fractal dimension of different types of landforms in Xisha Islands in the corresponding region is high mountain area > medium and low mountain area > basin area, which reflects the difference of surface roughness or complexity of different types of landforms. The calculated fractal dimension is helpful to reveal the heterogeneity of general geomorphological features in different development stages.