This study aimed to develop a novel neuromuscular coordination-guided rehabilitation exercise through human-machine interaction under isometric conditions and tested its effects on muscular coordination and clinical scores to improve motor function post-stroke. Six post-stroke survivors participated in a muscle synergy-guided exercise as a test group (n = 3) and a force strengthening-guided training as a control group (n = 3). One complete training set consisted of 18 one-hour training sessions for six weeks. Pre- and post-training assessments and one-month and three-month retention tests were performed using a custom-designed robotic device under isometric conditions. While the muscle synergy-guided test group improved intermuscular coordination and Fugl-Meyer Assessment scores, the force strengthening-guided control did not. This pilot study shows that abnormal intermuscular coordination can be malleable to be similar to healthy patterns through human-machine interaction, even for severely impaired survivors, and the therapeutic exercise has the potential to improve motor control in the upper extremity after stroke.