Numerous studies have discussed the economic impacts of the COVID-19 pandemic in recent years. However, the effectiveness and trade-offs of diverse countermeasures still need to be investigated, particularly under the long-term goal of low-carbon transition, which is crucial for understanding the potential impacts of the future public health emergency (PHE) related economic crisis. Given that China still faces big pressures from the potential PHE and carbon neutrality, this paper assesses the effectiveness of policy instruments in restoring the economy and advancing green development after the PHE using the Dynamic Stochastic General Equilibrium framework. Our findings reveal that the PHE imposes more constraints on the economy because of the decrease in productivity on the supply side and in consumption on the demand side. Compared to the other counterparts, the mixed stimulus can overcome the adverse impacts of the PHE while contributing to carbon reduction. Furthermore, all types of low-carbon policies investigated in this study can contribute to carbon reduction at the expense of economic growth. Meanwhile, the carbon tax realizes the target of reducing emissions with the smallest negative impact on economic growth. Thus, we suggest adopting the carbon tax policy as the most effective low-carbon measure to address uncertainties associated with the PHE.