Abstract: Natural gas is composed of some kind of low molecular hydrocarbon, but the accumulated natural gas in reservoir is mainly composed of methane generally. This paper studied the secondary migration characteristics of natural gas by the physical simulation experiment, and discovered that the secondary migration of natural gas is a kind of Intermittent Flow which developed from the alternation of Plug Flow and Preferential Flow.The Intermittent Flow of natural gas can cause heavier hydrocarbon captured and sealed off into rock pores with formation water. And then this paper discussed composition alternation mechanism of natural gas during secondary migration based on the analysis of hydrocarbon formation and the relationship of gas, water and rock. It is resulted that the composition differentiation in the secondary migration of natural gas, heavier hydrocarbons captured and sealed off into rock pores caused the Intermittent Flow of natural gas and the dissolution of oil preserved in the secondary migration path are main reasons why the accumulated natural gas is composed of much more methane.