Invasive right-sided heart catheterization (RHC) is currently the gold standard for assessing treatment effects in pulmonary vascular diseases, such as chronic thromboembolic pulmonary hypertension (CTEPH). Quantifying morphological changes by matching vascular trees (pre- and post-treatment) may provide a non-invasive alternative for assessing hemodynamic changes. In this work, we propose a method for quantifying morphological changes, consisting of three steps: constructing vascular trees from the detected pulmonary vessels, matching vascular trees with preserving local tree topology, and quantifying local morphological changes based on Poiseuille’s law (changes in radius-4,△r-4). Subsequently, median and interquartile range (IQR) of all local △r-4 were calculated as global measurements for assessing morphological changes. The vascular tree matching method was validated with 10 synthetic trees and the relation between clinical RHC parameters and quantifications of morphological changes was investigated in 14 CTEPH patients, pre- and post-treatment. In the evaluation with synthetic trees, the proposed method achieved an average residual distance of 3.09±1.28 mm, which is a substantial improvement over the coherent point drift method (4.32 ± 1.89 mm) and a method with global-local topology preservation (3.92 ± 1.59 mm mm). In the clinical evaluation, the morphological changes (IQR of △r-4) was significantly correlated with the changes in RHC examinations, (Formula Presented). Quantifying morphological changes may provide a non-invasive assessment of treatment effects in CTEPH patients, consistent with hemodynamic changes from invasive RHC.