The invention relates to a computer program, more specifically to a method for quantitatively analyzing RNA mutation harmfulness. The invention aims to provide a quantitative method capable of analyzing RNA mutation harmfulness simply, conveniently and quickly, solves the problem that mutation harmfulness is difficult to evaluate, quantify and analyze, reaches the objectives of analysis and prediction of RNA mutation harmfulness, thus improving the understanding of RNA mutation and RNA evolution. The invention provides a method for quantitatively analyzing RNA mutation harmfulness for a computer system, which fuses site structure harmfulness information with site sequence harmfulness information, quantitatively analyzes RNA mutation harmfulness, and gives a quantitative analyzing result of RNA mutation harmfulness.