To use cardiac magnetic resonance imaging (MRI) to investigate the effect of balloon pulmonary angioplasty (BPA) on interventricular dyssynchrony and its associations with ventricular interaction, which impairs LV function in patients with inoperable chronic thromboembolic pulmonary hypertension (CTEPH). This prospective observational study was approved by our institutional review board. Cardiac MRI and right heart catheterization were conducted before BPA sessions and at the follow up after BPA in 20 patients with CTEPH. We measured right ventricular (RV) and left ventricular (LV) end-diastolic volume (EDV), end-systolic volume (ESV), stroke volume (SV), and ejection fraction (EF) using MRI. For the LV and RV free walls, the time to peak (T_peak) of circumferential strain was calculated as a parameter for interventricular dyssynchrony. Following BPA, the RV-EDV and -ESV were significantly decreased, and the RVEF was significantly increased. Conversely, BPA led to significantly increased LV EDV and SV without changing LVESV. The left-to-right free wall delay (L–R delay) in T_peak strain decreased from 105 ± 44 ms to 47 ± 67 ms (p < 0.001). Increased LV EDV (r = 0.65, p < 0.01), SV (r = 0.74, p < 0.001) and 6-minute walk distance (6MWD) (r = 0.54, p < 0.05) were correlated to the reduction in L–R delay. In patients with inoperable CPEPH, BPA improved interventricular dyssynchrony, which was strongly associated with increased SV and 6MWD. The assessment of interventricular dyssynchrony using cardiac MRI has an important role in evaluating ventricular interaction, which reduces LVSV and exercise tolerance.