There is an increasing demand for large bandwidth signal testing in the fields of new generation wireless communication, internet of things and virtual reality, etc. Signal analyzers are the primary tool for studying the spectral composition of signal. To enhance the large bandwidth signal testing capability of signal analyzers, a wideband signal acquisition system based on digital bandwidth interleaving is studied and designed; aiming at the problem of deterioration of the in-band frequency response caused by the gain imbalance of each channel of the acquisition system and stitching of frequency bands, a method of correcting the in-band frequency response error by designing a compensation filter based on multi-carrier testing and the least squares method is proposed. The actual experimental results show that the designed system can effectively improve the signal analyzer’s analysis bandwidth. The in-band amplitude flatness of the 1.8 GHz bandwidth acquisition system is ±0.97 dB, the phase linearity is ±0.11 rad, and the in-band frequency response error correction effect is better than the mainstream method of frequency sampling method.