Abstract: The land quota trade fully optimizes the rural element allocation scope and element organization mechanism. It effectively eases the problems between shortage of urban construction land and idle rural construction land. However, with the land quota trade progressive development, disadvantageous factors arising from the risks of protection of cultivated land and of farmers' rights and interests constrain land quota trade from further promotion. The text takes the potential risks in land quota trade system in Chongqing municipality as research object and conducts an empirical study on the potential risks in land quota trade system, so as to provide micro data support in building risk prevention system in land quota trade.