The balanced field electromagnetic technique as an effective in-line inspection method for cracks in long-distance oil and gas pipelines uses the pipeline inspection gauge (PIG) as the detection tool. PIG is characterized by the employment of a large number of sensors, but as each channel uses its crystal oscillator as a signal source, it inevitably generates frequency difference noise, which affects crack detection. A method of eliminating the frequency difference noise by using same-frequency excitation is proposed to solve the problem. Combining the principle of electromagnetic field propagation with the detection signal processing process, the formation process and characteristics of the frequency difference noise are theoretically analyzed, and the specific impact of frequency difference noise on crack detection is analyzed. The method of unified clock excitation for all channels is adopted, and a same-frequency excitation system is developed. The correctness of the theoretical analysis and the validity of the proposed method are verified by platform experiments and pulling tests. The results show that the effect of the frequency difference on noise follows the whole detection process, and the smaller the frequency difference, the longer the noise period. The frequency difference noise distorts the crack signal and is of comparable magnitude to the crack signal, which tends to drown out the crack signal. The same-frequency excitation method can eliminate frequency difference noise at the source and has a high signal-to-noise ratio. The method can provide a reference for multi-channel frequency difference noise cancellation in other AC detection technologies.