In the transition to a low-carbon economy, the market share for renewable energy is significantly increasing and gradually substituting traditional energy. The high renewables penetration results in increased balancing action volumes due to system stability requirements. The balancing market (BM) primarily turns down renewable generation and turns up traditional carbon-intensive generation in response to real-time energy imbalance. Existing dual-stage market mechanisms conflict with the carbon reduction trajectory by implementing balancing actions regardless of their carbon footprint. This paper proposes a novel balancing market model by evaluating the negative externality of carbon to coordinate the environmental targets in both markets. Firstly, mathematical models are formulated for key participants in the dual-stage market. The emissions of dispatchable generators and flexible loads are distinguished by their operation modes and flexibility types, respectively. Carbon signals are incorporated into their bid/offer pricing models through the carbon emission flow (CEF) model. By integrating these incentives for carbon reduction, the dual-stage market model is formulated to minimize economic and environmental costs. Simulation results demonstrate that the proposed model effectively reduces carbon emissions in the BM and strike a balance between cost-efficiency and environmental benefits. It enables system operators to incentivize decarbonized energy resources in both stages.𝑇 /,1'2 +2 , 𝑇 /,1'2 +,, Minimum startup and shutdown time for generator 𝑔 𝑈𝑜𝑆 Use of system charge 𝑟 6>8 ,𝑥 6>8 Resistance and reactance of line 𝑏, 𝑗 𝜇 Generation efficiency