<p>The densely developed bedding-perpendicular joints (BPJs) in the sand-mudstone interbedded strata in the Ordos Basin exhibit significant heterogeneity distribution. The interface morphology affects the heterogeneity development of joints. Combining in-situ investigations, 3D-printed physical model experiments, and numerical simulations, the progressive filling process of BPJs has been reproduced, revealing the influence of interface morphology on the development of BPJs. The findings indicate that rough interface morphology reduces the spacing between BPJs and delays the gradual saturation process of joints. This was supported by a negative exponential relationship between roughness and joint spacing. Additionally, there was a positive correlation between roughness and the skewness of the normal distribution of joint spacing. The concave interface of the hard/sandstone layer typically induces stress concentration, resulting in more joints cracking near it. An increase in the thickness of the hard layer leads to a decrease in stress concentration in the concave interface area and weakens the densification effect of roughness on BPJs. An increase in the tensile strength of hard layers enhances the stress concentration resistance capability of the depression zone, delaying joint development and reducing the probability of end fractures caused by rough interfaces.</p>