Arrival flight sequencing optimization is an effective method to improve the landing efficiency of incoming flights and reduce flight delays. Based on this, with the goal of maximizing landing efficiency, combined with multi-runway and multi-route selection, and considering the actual waypoint restrictions, a mixed integer programming model for multi-path and multi-runway integrated arrival flight sequencing optimization is proposed. In order to solve the real-time problem of large-scale flight sequencing calculation, a multi-waypoint rolling horizon control algorithm is proposed. The terminal area of Guangzhou Baiyun International Airport is used as an example for verification, and the actual arrival flight data is used to carry out calculation experiments. In terms of wake turbulence safety interval, the RECAT-CN operation standard is used. The calculation results show that when the number of small-scale flights (23 flights) is small, the maximum landing time of the proposed model is 55 s earlier than the first-come-first-served method and 271 s earlier than the non-optimized one; when the number of large-scale flights (104 flights) is large, the solver alone cannot find a feasible solution within 3600 s, and the proposed algorithm finds a solution within 128.65 s. The proposed model and algorithm are effective and can be applied to actual flight scheduling optimization.