Aircraft sequencing has the potential to decrease flight delays and improve operational efficiency at airports. This paper presents the aircraft sequencing problem (ASP) on multiple runways with complex interactions by allocating flights on runways and optimizing landing times, take-off times, and crossing times simultaneously in a uniform framework. The problem was formulated as a mixed-integer program considering realistic operational constraints, including runway assignment preferences based on the entry/exit fixes of the terminal maneuvering area (TMA), minimum runway separation, time window, and arrival crossing rules. Variable-fixing strategies were applied, to strengthen the formulation. A first-come-first-served (FCFS) heuristic was proposed for comparison. Various instances from the literature and from realistic data sets were tested. Our computational study showed that the solution approach optimizes runway schedules, to achieve significantly fewer flight delays, taking runway assignment preferences and arrival crossings into account.