Call auction and continuous auction are introduced into the domestic electricity market, which enrich the bidding mode, increase the transparency of market information, and improve the trading efficiency. However, they put forward higher requirements for its implementation algorithm, it is particularly important to find an efficient and reliable clearing algorithm. For this reason, a clearing algorithm which combines call auction and continuous auction is designed in this paper. Based on scalable multi-factor ordering, flexible market clearing, bidding order linking, dynamic priority queuing technology, the two-stage order linking is realized effectively, the clearing efficiency is improved, and the orderly and efficient development of the whole transaction is guaranteed. At present, the algorithm has been applied to the software platform of Kunming Electric Power Trading System, and its practicability and effectiveness have been verified by engineering.