Automatic assessment of the operation ability of operators based on computers is an essential approach for improving the effectiveness of equipment operation training and enhancing equipment safety. Present methods primarily focus on the operation results but pay less attention to the operation procedure. One reason is that there is a lack of a model that has the ability to describe all probable paths to accomplish the same task. Therefore, an operations chain model is put forward for the first time to describe the standard operation procedure and relationships among operations based on the decomposition of operational tasks and the relationships among the various operations required to fulfill the task. A specific operation task corresponds to an operations chain, which will form one or multiple standard operation sequences that will allow trainees to complete the same task through different paths. The Needleman–Wunsch sequence alignment algorithm is introduced to match the trainees’ operation sequence with all standard sequences. The maximum alignment result is the score of the trainees’ operations. An example shows that the operations chain model can accurately describe the complex structure of the standard operating procedures. The Needleman–Wunsch sequence alignment algorithm can objectively evaluate the trainee’s operation capabilities. The combination of the operations chain model and sequence alignment algorithm can form a complete operation procedure assessment method that is friendlier to trainees and has more objective evaluation results. The method will help to improve the effectiveness of the competency assessment of equipment operators.