The invention discloses a method for modular multiplication remainder input side channel energy analysis attacks aiming at M-ary implementation of an RSA cryptographic algorithm. The core of the method is that when M-ary implementation is used by modular exponentiation, modular multiplication remainder input serves as an attack target to implement CPA (correlation power analysis) attacks. The method comprises the steps that (1) signals are acquired, and a sampling matrix is established; (2) the modular multiplication remainder input is selected to serve as the attack target; (3) a correlation model is determined; (4) cycle index values are guessed, and a median matrix is calculated; (5) a simulated energy consumption matrix is calculated; (6) linear correlation coefficients between corresponding measuring points in the step (1) and the matrix determined in the step (5) are calculated, correct modular multiplication remainder input values of all cycles are attacked, and all corresponding correct cycle indexes are found out, and are connected in series, so that a complete index is obtained. According to the method, a novel M-ary side channel attack method is provided, and the flexibility, the effectiveness and the success rate of RSA cryptographic algorithm analysis attacks are improved.