To fully unleash the emission reduction potential of virtual power plant （VPP） and tap into the potential profits of clean energy, a source-load low-carbon economic dispatching model based on the secondary carbon market and green certificate allocation system is proposed. Firstly, aiming at the hub that aggregates various energy devices within VPP, the optimization objective is to minimize the comprehensive operation and maintenance costs. Secondly, a secondary carbon market trading system based on carbon quota trading and auction markets is established to simulate the incomplete information game involving multiple enterprises on the source side. Thirdly, based on carbon flow theory, carbon emissions and carbon flow density are combined into a carbon indicator, and a green certificate allocation method for the load side is established to improve the economic benefits of users purchasing green certificates, thereby enhancing the value of green certificates and benefiting clean energy enterprises that provide them. Finally, a multi-region VPP model is used as an example to simulate typical days in summer and winter. The results of the case study verify that the secondary carbon market and green certificate allocation system can effectively utilize market transmission mechanisms to increase the revenue of environmentally friendly enterprises and encourage high-carbon emitting enterprises to transition towards low-carbon operations.