Aiming at the problems of high error rate and long time of traditional environmental pollution control cost accounting algorithm, a cost accounting algorithm of environmental pollution control based on discrete probability was designed. Firstly, the cost of environmental pollution is classified and the monetization function of environmental pollution cost is constructed. Then, the cost accounting index system of environmental pollution control is established, and the cost function of environmental pollution control is constructed. Finally, a discrete probability model is used to optimize the cost function, and the optimized cost function is used to design the environmental pollution control cost accounting algorithm. The experimental results show that the proposed algorithm can quickly converge to the optimum within 70 iterations, the accounting error rate is between -0.2% and 1.3%, and the accounting time is always less than 0.4 s. It has good convergence and can accurately calculate the cost of ecological environmental pollution control.