The impacts of technologies such as hydrogen energy and carbon capture on the operation of micro-energy grids were considered, and the system structure of micro-energy grids with multi-energy conversion of hydrogen, heat, electricity and gas was constructed. The influence of the launch of China certified emission reduction (CCER) trading on the transaction and operation of micro-energy grids was analyzed, and the cost and benefit of micro-energy grids under the coupling of the electricity-carbon-green certificate market were calculated. On this basis, a two-stage multi-timescale rolling optimization model was constructed. The day-ahead hourly scheduling scheme was formulated, and intra-day rolling optimization was realized with real-time scenic energy data updated at a 15 min timescale. Scenario-based control method was adopted for numerical simulation. The results indicate that the hydrogen energy module can reduce the power purchase cost and demand response cost of micro-energy grids. With the improvement in the energy conversion efficiency of the hydrogen module, the overall operational cost of micro-energy grids can be effectively cut down. When the carbon allowance price is higher than the green certificate price, micro-energy grids tend to apply for CCER certification and issuance to offset excessive carbon emissions, or sell surplus CCER quotas for additional revenue. Furthermore, rolling optimization can efficiently revise the output of each energy unit, thereby improving the economic performance of micro-energy grid operation.