It is well known that there are several vertical flight phases for the aircraft in the flight. The cruise flight phase takes most of the flight time, flight distance and fuel consumption, so it is important and necessary to develop the FMS vertical trajectory prediction algorithm for the cruise flight phase, aiming to improve the economy, comfort and safety of the flight. In order to meet the versatility of the vertical trajectory prediction algorithm between different types of aircraft in the cruise phase and improve the accuracy and reliability of the prediction, the algorithm of vertical trajectory prediction for cruise flight phase is proposed in this paper. By calculating the cruise speed profile and constructing the realistic atmospheric model of prediction, and then calculating the cruise fuel flow data based on the aircraft model of first-principles, the vertical trajectory prediction for the cruise phase is given by designing the vertical trajectory prediction algorithm logic. Finally, the effectiveness and accuracy of the algorithm are verified by ground simulation and air flight test. The results show that the vertical trajectory prediction algorithm of FMS cruise phase based on the aircraft model of first-principles can predict the cruise trajectory of the aircraft, and the prediction accuracy error is less than 1%.