Extracting muscle synergy from surface electromyographic (sEMG) signals has become a standard method for evaluating motor control strategies during exercise. While numerous studies have described the synergy of the upper extremity in various stretch and reach tasks, few have analyzed the relationship between task performance and muscle synergy. This study introduces an experimental device and analysis method for examining muscle coordination in joystick manipulation, specifically for pilots. In this study, eight healthy subjects performed joystick manipulation tasks involving isotonic exercises with three different load levels. EMG and acceleration data from ten muscles were recorded. The muscle synergy effect was extracted, and the correlation between muscle synergy similarity, manipulation performance, and interaction load was analyzed. The experimental data revealed that while manipulation performance varied under different loading conditions, there were no significant changes in the synergistic muscle structure. Significant correlations were found between the similarity of some synergistic muscle structures and manipulation performance. However, there was no strong correlation between individual action performance and the average similarity of their muscle synergy. The analysis indicated a fixed muscle synergy pattern during rocker manipulation, which remained independent of the rocker load level. A negative correlation was observed between muscle synergy similarity and manipulation performance, as well as between muscle co-contraction index and manipulation performance. These findings contribute to improving the ergonomics of the flight stick and suggest targeted muscle training methods to enhance the precision of flight maneuvers.