The vesicular structure of volcanic rocks may disrupt the fluid flow in fractures and make the mechanism of fracture flow more complicated. This study evaluated the characteristics of fracture flow associated with vesicular structure. To quantify the vesicular structure in the fracture surface, different arrangements and sizes of drilled holes were designed and manufactured in artificial single fracture samples and three associated factors of area ratio, depth, and diameter of drilled holes. A series of laboratory tests was conducted with different vesicular structure and fracture aperture. A nondimensional parameter, λ, was introduced to reveal the vesicular structure and the relationship between λ and the Reynolds number was established. The test results illustrate that the Reynolds number is sensitive to the vesicular structure in fracture surface. The vesicular structure could enhance the fracture flow rate when the flow rate is relatively small and vice versa. However, the fracture flow has no obvious change when varying each influencing factor related to vesicular structure separately. A new formula was obtained to estimate the fracture flow rate considering vesicular structure and the input variables contains fracture aperture and hydraulic gradient. The proposed formula was proven to be reasonable by comparing the measured data from the single fracture tests of real volcanic basalt samples.