Background: A variety of functional disorders can be caused after stroke, among which impairment of respiratory function is a frequent and serious complication of stroke patients. The aim of this study was to examine diaphragmatic function after stroke by diaphragm ultrasonography and then to apply to explore its correlation with extremity motor function and balance function of the hemiplegia patients. Methods: This cross-sectional observational study recruited 48 hemiplegic patients after stroke and 20 matched healthy participants. The data of demographic and ultrasonographic assessment of all healthy subjects were recorded, and 45 patients successfully underwent baseline data assessment in the first 48 h following admission, including post-stroke duration, stroke type, hemiplegia side, pipeline feeding, pulmonary infection, ultrasonographic assessment for diaphragm, Fugl–Meyer Motor Function Assessment Scale (FMA Scale), and Berg Balance Scale assessment. Ultrasonographic assessment parameters included diaphragm mobility under quiet and deep breathing, diaphragm thickness at end-inspiratory and end-expiratory, and calculated thickening fraction of the diaphragm. The aim was to analyze the diaphragm function of hemiplegic patients after stroke and to explore its correlation with extremity motor function and balance function. Results: The incidence of diaphragmatic dysfunction under deep breath was 46.67% in 45 hemiplegia patients after stroke at the convalescent phase. The paralyzed hemidiaphragm had major impairments, and the mobility of the hemiplegic diaphragm was significantly reduced during deep breathing (p < 0.05). Moreover, the thickness fraction of hemiplegic side was extremely diminished when contrasted with the healthy control and non-hemiplegic side (p < 0.05). We respectively compared the diaphragm mobility under deep breath on the hemiplegic and non-hemiplegic side of patients with left and right hemiplegia and found there was no significant difference between the hemiplegic side of right and left hemiplegia (p > 0.05), but the non-hemiplegic side of right hemiplegia was significantly weaker than that of left hemiplegia patients (p < 0.05). The diaphragm mobility of stroke patients under quiet breath was positively correlated with age and FMA Scale score (R2 = 0.296, p < 0.05), and significant positive correlations were found between the diaphragm mobility under deep breath and Berg Balance Scale score (R2= 0.11, p < 0.05), diaphragm thickness at end-inspiratory and FMA Scale score (R2 = 0.152, p < 0.05), and end-expiratory thickness and FMA Scale score (R2 = 0.204, p < 0.05). Conclusions: The mobility and thickness fraction of the hemiplegic diaphragm after stroke by diaphragm ultrasonography were significantly reduced during deep breathing. Diaphragm mobility on bilateral sides of the right hemiplegia patients were reduced during deep breathing. Moreover, the hemiplegic diaphragmatic function was positively correlated with extremity motor and balance function of the hemiplegia patients.