我國在1997 年憲改大幅調整中央政府體制，並將其修改為半總統制；類似法國「雙首長制」的制度。總統改為直接民選並且擁有實權，譬如總統擁有決定國家安全有關大政方針的決定權、總統任命行政院院長不須立法院的同意；但行政院仍為國家最高行政機關；以致於行政權歸屬不清。而且行政院須對立法院負責，立法院得對行政院院長提出不信任案；同時，行政院院長得呈請總統解散立法院。換言之，現行憲法規定只有在立法院倒閣後，總統才能被動的解散國會，這一點與雙首長制大不相同。此外，行政院對於法律案、預算案移請立法院覆議時，如經全體立法委員二分之一以上決議維持原案，行政院院長應即接受該決議。因而現行憲政體制的設計不但矛盾重重，在實際的操作上更是窒礙難行，尤其於2000 至2008年我國首次政黨輪替，也出現少數政府，政府就立刻面臨全面癱瘓的危機，憲法機制也無法解決行政權與立法權之間的摩擦。 綜言之，我國現行體制之總統和立法院之間存有潛在的不穩定的競爭；並且一旦總統與立法院的多數黨分屬不同的政黨時即形成相互對立。顯然由於我國第四次修憲制度設計的問題，加上欠缺成熟民主文化與憲政慣例，實已埋下憲政僵局的因子。基此，本研究以新制度主義為研究途徑，主要探討我國九七憲改後之總統、行政院與立法院間之權力架構下的運作與課責關係，並藉以檢視1996~2000 年李登輝－絕對多數政府（府會合一）時期；2000~2008 年陳水扁－少數政府（府會分裂）時期；2008 年~迄今馬英九－絕對多數政府（府會合一）時期等三階段之憲政運作；並且如何在憲政主義基礎上，進一步的制度調整，以符合民主憲政原理。

In 1997 constitutional amendments significantly adjusted the central government system to a system similar to the French dual executive system or semi-presidential system in Taiwan. The president shall be elected by direct popular vote and he possesses quite considerable powers, for example, the president may to determine major policies for national security；the president of the Executive Yuan be appointed by the president, requiring no consent of the Legislative Yuan. But the Executive Yuan shall be the highest administrative organ of the State. Therefore, the constitutional system causing ambiguity concerning the distribution of administrative power. Furthermore, the Executive Yuan shall be responsible to the Legislative Yuan. The Legislative Yuan may propose a no-confidence vote against the president of the Executive Yuan , and at the same time, the president of the Executive Yuan may request that the president dissolve the Legislative Yuan. In other words, current constitutional laws stipulate that only when the legislature overthrows the cabinet can the president exercise passively the power to dissolve the legislature. This differentiates Taiwan's constitutional system with that of the dual executive system. In addition, when the Executive Yuan request the Legislative Yuan to reconsider a statutory or budgetary bill. Should more than one-half of the total number of Legislative Yuan members uphold the original bill, the president of the Executive Yuan shall immediately accept the said bill.Therefore, not only the design of the current constitution is laden with contradictions and incompatibilities, its actual implementation is also morbidly inefficient, especially in 2000-2008 years, the first change of ruling party also appeared minority regime, the government faces immediate risk of a total shutdown, the constitutional mechanism provided was unable to resolve the friction between administrative and legislative power. In general, Taiwan's current constitution, it can create potentially destabilizing competition between the President and the Legislative Yuan. Any time we have a president and the legislative majority belonging to different political parties hostile to each other. Obviously the fourth constitutional amendment set the stage for a constitutional deadlock, and due to immature democratic culture and lack of constitutional convention. In light of this, this case study adopted systems approach, new institutionalism and jurisprudence of constitutional interpretation to survey what are the differentiates constitutional functioning among the Lee Teng-hui(majority regime), Chen Shui-bian(minority regime) and current president Ma Ying-jeou(majority regime). This article intends to explore the current constitution of relationships among President, Executive Yuan and Legislative Yuan in Taiwan.The major issue today is how to build upon constitutionalism already in place and establish stronger democratic constitutional governance.