Petroleum exploration has proved that carbonate rock is an important source rock but the mechanism of hydrocarbon generation carbonate rock have remained unclear.It is caused by the different way of hydrocarbon generation between carbonate and clay rock.Generally, diagensis is earlier than hydrocarbon generation in carbonate rock and later than hydrocarbon generation in clay rock.Based on the research of natural gas geochemistry in Sichuan basin,it is suggested that the most important research direction of petroleum geochemistry in carbonate rock includes evaluation of carbonate source rock,effective migration and accumulation system of natural gas,and gas reservoir geochemistry in carbonate rock.