Understanding droplet migration in stenosed microchannels is crucial for various applications. This study explores how droplet properties (viscosity, surface tension, density, and diameter) and channel characteristics (stenosis degree and wall elasticity) affect droplet movement and blockage in deformable stenosed microchannels. Higher viscosities lead to lubrication film formation between droplet and wall, reducing viscous resistance, while increased surface tension enhances wall adherence, amplifying Laplace pressure. Droplet entry is primarily influenced by viscosity, while passage is governed by surface tension and curvature effects at the droplet–wall interface. Surface tension dominates pressure generation in the channel and within the droplet, influencing wall deformation and hydrodynamic resistance. The study examines the relationship among droplet viscosity, density, surface tension, channel wall elasticity, and the maximum capillary number (Camax) on the lubrication film thickness between the droplet and the channel wall. A lubrication film exists for Camax≥0.095, reducing blockage chances. A critical range of the modified Ohnesorge number Oh*×1000≤132 and the capillary number (Camax<0.095) indicates higher chances of droplet blockage. The blockage prediction method based on the modified Ohnesorge exhibits a sensitivity of 100%, specificity of 92.6%, and accuracy of 95.9%. Additionally, the study explores the impact of channel wall elasticity on droplet entry, transit, and hydrodynamic resistance. Higher wall elasticity facilitates faster entry but introduces curvature during passage, increasing frictional resistance and blockage likelihood as the wall softens.