Abstract: With the carbon peak and carbon neutrality goals being advanced, low-carbon development is an important pathway for Beijing’ s Ecological Conservation Area to fulfill its capital functional positioning and to reconcile ecological protection with economic development. The region has made notable progress in ecological restoration and low-carbon industry cultivation, yet it still faces structural problems such as ineffective realization of ecological product value, mismatches between input supply and demand, and insufficient institutional incentives. Based on a “value-inputs-governance” analytical framework, this paper examined the main dilemmas and causes of the region’ s low-carbon development, and proposed three optimization pathways: refined operation of ecological assets, energy system optimization coupled with industrial upgrading and integration, and carbon inclusion mechanism building together with governance system improvement. Furthermore, it offered policy recommendations to improve the support system from four aspects: fiscal finance, ecological compensation, industrial policy, and collaborative governance. This paper provides a reference for ecologically sensitive areas in mega-cities to advance low-carbon development and practice the “Two Mountains” theory.