Side-polished coupling cannot damage the central air hole of capillary optical fiber(COF), so that COF can be conveniently used as atomic guiding or sampling tube. Side-polished coupling of single mode fiber and a novel COF is studied by experiment. And the results prove the coupling method is feasible. By analytical equations, the quantitative relationship between the thickness of the residual cladding and the coupling optical power is calculated. It may be the basis for further study on the side-polished coupling for COFs. Side-polished coupling method also can expand the application of COF or other similar microstructure fiber.