A novel mismatch correction strategy is proposed for bandwidth-interleaved (BI) acquisition system with overlapping band. In the proposed strategy, mismatch errors due to the nonuniformity among different subbands are considered as phase misalignment and magnitude distortion, which are estimated and corrected separately. Taking advantage of the characteristics of overlapping band, phase misalignment is estimated by homomorphic correlation analysis of the signal in the overlapping band and compensated before subband merging. Magnitude distortion is compensated by an FIR filter designed with frequency sampling method after subband merging. Compared with other conventional methods, this strategy can realize nearly perfect reconstruction (NPR) without transfer function to be known or any additional hardware. The proposed strategy has been validated via simulations of a BI system with 2GHz bandwidth.