The ergonomics level of pilot operation procedures is very important for the operational safety of the aircraft, and the evaluation of the current pilot operation procedures is usually carried out at the end of the design, which brings a great increase in the cost of design iteration, so it is necessary to consider the completion of evaluation and design iteration work in the early stage of design. Therefore, this study first analyzes the design process, design elements and key points of ergonomic evaluation in the design of pilot operation procedures, and then analyzes the correspondence between the key elements of operation program design and the elements of colored Petri net, and proposes the expression of the operation program design scheme and the model expression of key ergonomic evaluation based on the colored Petri net in the early stage of design. Finally, the colored Petri net modeling was conducted on the emergency descent program of a large passenger aircraft, and the key ergonomic evaluation results of the program were obtained based on the model. This study provides a model for the design in the early stage of pilot operation program design, which can realize the modeling the expression of the design program and generate the corresponding ergonomic evaluation results to guide the design iteration.