Due to the poor detection and suppression effect of signal harmonics in grid connected equipment by traditional methods, the calculation efficiency is reduced and the control result is not ideal. A multi-objective cooperative control method of grid connected equipment based on sliding iterative discrete Fourier is proposed. Based on the discrete Fourier analysis of the sliding iteration, the sliding window iteration is used to separate the fundamental component and harmonic component of the current signal in the grid connected equipment. According to the separation results, the expressions of the instantaneous power and reference current of the grid connected equipment are obtained, the optimization factor is introduced to obtain the unified expression of the reference current, and the multi-objective function containing the optimization factor is constructed, The Drosophila algorithm is used to solve the objective function, and finally realize the multi-objective cooperative control of grid connected equipment. The experimental results show that the proposed method can quickly and accurately complete the multi-objective cooperative control of grid connected equipment.