Spermidine (SPD) is an important signal molecule relate to protein food safety, but vulnerable to interference during detection. Here, an electrochemical sensor system for the spermidine detection was developed by a self-assembled molecularly imprinted polymer (MIP) film coated on disposable screenprinted electrodes. The modification imprinted polymer was prepared with template molecules SPD and functional monomer meth acrylic acid (MA) with molar ratio 1:4 through ultraviolet polymerization. The cyclic and differential pulse voltammetry (CV and DPV) scanning showed that the best adsorption equilibrium time of the modified electrodes was 360 s. The electrodes exhibited good linear relationship ranging from 1.0 × 10 −6 mol/L to 5.0 × 10 −6 mol/L (y = −1.22x+7.82, R 2 = 0.9952), and the detection limit was 1.7016 × 10 −7 mol/L. When take high concentration of histamine and tyramine as interfering components, the modified electrodes detection relative standard deviation was < 5% and thus proved good anti-interference ability. In addition, the density function theory (DFT) calculation explored the intera-molecular interaction of SPD-MA imprinted complex, and the simulation showed that the prepared device can keep recognition stability under the potential difference stress range from 0 to 0.005 a.u. Therefore, the prepared system has the potential for rapid detection spermidine in the place.