Abstract: A non-proportional modal damping model was proposed by the nodal mode-damping-ratio of a finite element model. The efficient algorithm of the damping force was presented in a nonlinear explicit format. Base on practical engineering, the stability of the explicit format was analyzed. The non-proportional damping model and efficient algorithm were implemented in CPU+GPU parallel nonlinear software. The dynamic time history response of a super high-rise steel-concrete structure, Guangxi Dongmeng tower, with millions degrees of freedom was analyzed by this software. The efficiency of parallel algorithms and the effect of non-proportional damping on the dynamic response of the structure were studied.