Abstract: Previous studies usually divide a statistical analysis model of the settlement in high core rock-fill dams into filling factors, aging factors, and water pressure factors, taking a dam block as a homogeneous body. Such a simplification ignores the influence of nonuniformity in settlement deformation caused by the differences in construction quality. This study develops a settlement deformation analysis model for the dams of this type to take into account the real-time construction quality factors together with the factors of filling, aging and water pressure, based on an analysis of stress and deformation in the filling body. This multi-parameter nonlinear model is combined with a M5’ model tree in simulation of the dynamics of settlement deformation. It combines the advantage of such a tree in solving global nonlinear problems and the fast convergence of a particle swarm optimization algorithm in solving multi-parameter problems, and thus it is able to fit and predict the settlement process. We compare it with a traditional analysis model excluding construction quality factors and a multiple linear regression analysis model. Results show that this new model is the best in terms of absolute errors and square sum errors in calculation of the settlement deformation and comprehensive index but its correlation degree remains as low as those of the other two models. This study suggests that modeling the real-time construction quality factors provides more reliable and objective analysis on the settlement deformation of high core rock-fill dams.