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Fractional differential equations are one of the important contents of advanced mathematics courses. The article uses fractional differential equations to describe the effects of children’s innovative education courses. Through the qualitative analysis of the basic model, several conditions to ensure the effect of children’s innovative education courses are obtained. At the same time, combined with practical experience, the teaching curriculum case design analyzes the specific application of the fractional differential equation in the effect of children’s innovative education curriculum. Research has found that the fractional differential equation algorithm improves the efficiency of innovation.