The Cooper-Harper rating of aircraft handling qualities has been adopted as a standard for measuring the performance of aircraft since it was introduced in 1966. Aircraft performance, the ability to control the aircraft, and the degree of necessary pilot compensation are three major key factors for deciding the aircraft handling qualities in the Cooper-Harper rating scheme. We formulate the Cooper-Harper rating scheme as a fuzzy rule-based system and use it to analyze the performance of the aircraft controller. The automatic estimation of the current system-level handling quality provides valuable up-to-date information for diagnostics and vehicle health management.