This study applies the Discrete Element Method (DEM) to analyze small strain characteristics of gap-graded soils, focusing on particle property disparities between coarse and finer particles. It extends the conventional small strain probe method to assess stiffness distribution in gap-graded specimens, distinguishing between different contact and particle types. Key findings reveal that the disparity in particle properties minimally affects void ratio and coordination number across various densities and stress levels. This disparity also shows limited impact on particle-scale stress transmission, supporting the validity of models with equivalent coarse and finer particle properties. A significant advancement is the adapted small strain probe method, which effectively measures stiffness distribution and demonstrates the role of finer particles, showing that the contribution of finer particles to the small strain stiffness is consistently lower than their volume fraction. This method also captures the effects of particle property disparity on small strain stiffness, demonstrating that higher particle Young’s modulus values in finer particles correlate with increased small strain stiffness contribution. While their overall impact on stiffness is less significant compared to that of stress transmission. This research introduces a simplified approach for analyzing stiffness distribution in gap-graded soils, enhancing understanding of gap-graded soils under diverse conditions.