Abstract: The conflict of criminal jurisdiction between the two sides of the Taiwan Straits stem from their legislative differences. The conflict caused by such differences result in the two sides’failure to recognize each other’ s criminal judgment and in dual decisions to repatriated criminals. This situation is contrary to the legal principle of prohibition against double jeopardy；it is also a hindrance to the development of the cross-strait judicial cooperation. To resolve this conflict，it is time to put on the agenda the establishment of a mechanism for joint criminal jurisdiction；the key point is to specify the division of jurisdiction for each side so that both sides will recognize and implement the court’s criminal decision of the other side. Thereby，a coordinated cross-strait judicial system and a benign interaction are expected to be established.