Clogging represents a critical challenge that undermines the efficiency and sustainability of drip irrigation systems by inducing uneven water distribution and increasing maintenance requirements. In this study, the phenomenon of clogging in drip emitters was investigated via computational fluid dynamics (CFD) in conjunction with the discrete element method (DEM). The original drip (OD) was analysed to pinpoint areas prone to particle accumulation, particularly in regions characterised by low velocity and reduced turbulence kinetic energy, conditions that facilitate particle deposition. The analyses revealed that vortex formation in narrow corners and stagnation zones within the emitter’s flow path primarily contributed to clogging. To address this issue, a modified drip (MD) was proposed, aimed at optimising flow patterns and mitigating vortex development. CFD–DEM simulations of the MD indicated a significant reduction in clogging risk and enhanced particle transport efficiency. At an inlet water velocity of 0.075 ms−1, the MD achieved a 2% higher particle transport rate than did the OD, and similar improvements were noted at higher velocities. These findings underscore the potential of design modifications to enhance system performance and reduce maintenance costs. Future research should further validate the MD under diverse environmental conditions, including variable water qualities and different soil types.