馬英九政府執政之後，兩岸關係發展愈趨緊密，航運、司法互助、金融合作、旅遊、食品安全衛生等協議陸續簽訂，可以說兩岸交流已經從消極、非正式的摸索，邁向積極、正式的書面協定。由於對國家定位的認知不同，兩岸對於彼此交流的法制架構也存在重大差異。相較於一般分裂國家的互動模式，兩岸之間將逐漸面臨法制落差所衍生的問題。本文從1994年辜汪會談所簽署的「兩會聯繫與會談制度協議」出發，以文本比較的方式，具體描述兩岸之間在協議主體、授權範圍以及內容與履行等方面的變化，並指出中國大陸的法制現狀，相對於台灣而言，更顯模糊與不確定。兩岸當局應及早正視兩岸交流所產生的法制落差格局，期使兩岸交流獲得長期穩定。

Since the Ma administration took on board, the development of the relationship between the Cross-Strait becomes closer and closer than before. The agreements related to the transportation, judicial assistance, financial cooperation, travel, food safety were signed. The communication of Cross-Strait governments has moved forward from passive and informal to positive and formal written record. Due to the great diverse regarding the definition of status quo, the Cross-Strait governments also have obvious discrepancy on the treatment of the signed agreements with the different legal system. Comparing with the experience and interact of other divided nations, it is no doubt that the Cross-Strait governments will have the forthcoming legal disputes in the near future. Based upon the "Agreement of liaison and colloquy mechanism between the two civil representative organizations in 1994." this article tried to describe the development and challenge of the Cross-Strait relationship by reading into the different texts of agreements. Briefly speaking, the legal system in Mainland China is relatively obscure and uncertain comparing with the one in Taiwan. This article also pointed out that the Cross-Strait governments should seriously look squarely at the difference of legal system on both party and assures the long-term stability of the written agreement.