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In this research, the effects of three amino acids, which are glutamic acid (Glu), lysine (Lys), and glycine (Gly), on the pasting and short‐term retrogradation properties of rice starch (RS) were studied. The mechanism of amino acids affecting the pasting and short‐term retrogradation properties of starch was further examined based on the molecular dynamics (MD) simulation method. It was revealed that the addition of Glu and Lys decreased the peak viscosity and increased the pasting temperature of RS, while Gly showed little or no obvious effect on the pasting property of RS. FTIR and X‐ray diffraction data showed that short‐term retrogradation of rice starch gels were restrained by supplement of Gly, Lys, and Glu. MD simulations indicated that compared to Gly, Glu, and Lys had better abilities to obstruct the pasting of starch system and delayed its short‐term retrogradation. The observed results of RVA, XRD, and FTIR showed different effects of the three amino acids (Glu, Lys, and Gly) on the pasting and short‐term retrogradation properties of rice starch, which corresponded to the calculation of the molecular dynamics. Furthermore, the result indicates the feasibility of predicting the behavior of amino acids and starch fractions in water based on the MD simulation method.