國內海洋法要如何與國際海洋法接軌，一直是法界所關注的議題；我國有關臺灣海峽航行制度的規範，受制於兩岸關係的特殊性與本身地貌的複雜性，使得許多法律見解仍莫衷一是，有待釐清。基此，本文將討論臺灣海峽的法律定位以及其所適用的航行制度種類，再依船舶類型區分為外國船舶與大陸船舶，繼以宏觀的角度，兼顧法理與國家利益，探討澎湖水道、領海、鄰接區、專屬經濟海域，與禁、限制水域等不同水域的較適航行制度。本文認為外國船舶航經臺灣海峽可排除過境通行的適用，而在澎湖水道及領海部分，宜容許外國船舶享有無害通過的權利；在專屬經濟海域則可思考增加有關海洋環境的保護和保全之相關規範。另針對大陸船舶，或可修改相關處置作法，以降低兩岸發生衝突的機會。

Introducing the UNLOS into the domestic Law of the sea has never been an easy work. Due to the peculiar cross-strait relations and complicated geographic features, the navigation regimes in Taiwan Strait can be interpreted in many different ways. Under these circumstances, this article differentiates between foreign and Chinese mainland vessels in different waters, such as internal waters, territorial sea, contiguous zone, EEZ, restricted waters, and prohibited waters within Taiwan Strait, and discusses their appropriate legal status individually. This article further argues that the transit passage is not appropriate for Taiwan Strait, and the innocent passage of foreign vessels might be permitted in both Pescadores Channel and territorial sea. It also suggests that protection and preservation of the marine environment should be considered to regulate further in the “Law on the Exclusive Economic Zone and the Continental Shelf of the Republic of China”. Furthermore, it would be helpful to revise the enforcement means upon Chinese mainland vessels for reducing possible conflicts between two sides of Taiwan Strait.