Permeability is a crucial parameter to evaluate the ultra-low permeability reservoir. The permeability of ultra-low permeability core samples was tested by using both nitrogen and helium. The factors affecting permeability were analyzed, including fluid types, displacement pressure, slippage effect, and their interaction. The research indicates that slippage effect exists, when the permeability is tested by either nitrogen or helium, however, there are differences in the results. With the same displacement pressure, the permeability tested by helium is bigger than that tested by nitrogen, and the differences are even more significant for the lower pore pressure. It is indicated that when helium at low pore pressure is used for the test, the slippage effect makes a bigger contribution to the permeability, since the diameter of helium molecules are smaller, and the molecular free length is longer. Slippage effect is stronger, especially for the lower permeability core samples.