In China, ecological damage compensation refers to the punitive ecological compensation for ecosystem damage by human activities, and it internalizes negative externalities by adjusting the interest relationship between ecological protectors and destroyers. Making reasonable and scientific payment standard of ecological damage compensation is an important factor to implement ecological damage compensation mechanism. Here, we take the forest ecosystem damage due to engineering projects in Guangdong Province, China as an example to discuss a calculation method for this compensation. Based on the forest ecosystem service (ES) value, this method comprehensively measures the degree, area, and duration of forest ecosystem damage due to various engineering projects. The contribution of construction projects to socioeconomic development and the importance of ecologically sensitive areas is also considered. Finally, a rapid, quantified, and differentiated compensation standard for ecological damage is obtained. This standard provides a scientific basis for balancing the interests between ecological protection and economic development. Thus, our results have certain guiding significance for the protection and sustainable development of the various types of ecosystems.