Oropharyngeal dysphagia is common after a stroke. Understanding the physiology of swallowing and its coordination with respiration in stroke recovery is crucially important. A non-invasive swallowing assessment method was used to detect oropharyngeal swallowing and respiration coordination simultaneously during the swallowing process. This system detected movement of the larynx, submental muscle activity, and nasal airflow. Six different sizes of water boluses (maximum of 20mL) were swallowed and assessed for each subject. We recruited 59 healthy participants and 38 first ever unilateral stroke patients completed baseline and follow-up assessments at 3, 6, and 9months poststroke. The results showed that oropharyngeal swallowing parameters in unilateral stroke deviate from normal patterns. For respiration coordination, the unilateral stroke group had longer swallowing apnea duration but similar frequencies of pre- and postswallowing respiratory phase patterns compared with the healthy controls. The probability of piece-meal deglutition was higher in the stroke group than in the control group. Additionally, there were gradually decreasing piece-meal deglutition probabilities among the stroke patients at follow-up, and none differed statistically from those of the controls at 6months poststroke. The non-invasive swallowing and respiration assessment method applied in this study detected the changes manifested in swallowing and respiration during the subacute phase of recovery in 6months after a unilateral stroke. The study results serve as a baseline for further research and help advance dysphagia research methodologies. These assessments may be combined with bedside evaluations for clinical application.