Understanding the emergence and selection of nucleic acids under prebiotic conditions is central to origins-of-life research. We developed a stochastic simulation framework to test whether DNA can outcompete RNA under moderate hydrothermal conditions due to differential stability and polymerization. The model incorporates Fe²⁺-catalyzed degradation, clay-enhanced polymerization, and thermal gradients, simulating 100 independent trajectories of polymer dynamics. DNA fraction rises above 0.5 within ~6–7 days in most simulations, with stochastic variability reflecting natural prebiotic fluctuations. The findings provide quantitative support for DNA’s selection potential under hydrothermal conditions, bridging theory and experimentally testable predictions