The fault structure is well developed and has an important role for controlling hydrothermal mineralization in Altay, Xinjiang, China. The fractal analysis indicates that faults and deposits spatially are all multifractal distribution. Large singularity exponent and high multifractal spectrum of faults show that the fault structure has high degrees of maturity and good linkage, facilitating fluids flow and controlling hydrothermal mineralization. The multifractal distribution of faults results in multifractal distribution of hydrothermal mineralization and ore deposits. Numerical simulation indicates that the strong coupling among faulting, lithology and fluids existed and resulted in different fracture permeability in different fractured rocks.