<p>Marine ecosystem services (MES) provide food, a comfortable environment, and recreational value to humans, but they are increasingly being degraded by human overexploitation and utilization. Marine protected areas (MPAs) are a critical means of safeguarding ecosystem services. Based on the logical relationship between the ecosystem service value of MPAs and ecological protection compensation, this study calculates the ecosystem service value of the provincial seal nature reserve in China’s Miaodao Islands and analyzes the compositional characteristics and spatiotemporal changes of this value, from which a scientifically grounded ecological compensation standard is established. This article highlights that, within MPAs, the proportion of material ecological products capable of achieving market value transformation remains relatively low. Conversely, the value of regulating, supporting, and underdeveloped cultural services—those yet to undergo market value realization—constitutes a comparatively higher proportion. Therefore, the establishment of MPAs can affect the composition of ecosystem service values in the region, thereby threatening the equal development rights of various stakeholders. This study concludes that when the level of economic development remains constant, as measured by gross domestic product (GDP), the greater the value of ecosystem services that cannot be converted into market value, the higher the priority for ecological protection compensation. Consequently, there is a greater demand for and a higher amount of ecological compensation. The main contribution of this research is the establishment of a strong correlation between the benefits of ecological protection and the entities responsible for compensating for ecological protection.</p>