As research into data centers progresses, the importance of resonant switched-capacitor converters in power supply design becomes more evident. Practical applications reveal that the values of resonant capacitors and inductors may deviate from their nominal values due to various factors, leading to resonant frequency instability. This instability poses a challenge to power electronics technology, affecting system reliability and performance. This paper analyzes the effect of frequency deviation on system functionality, identifies the relationship between output voltage and switching frequency, and proposes a self-tracking frequency strategy to address this issue. Through experimental validation, this approach shows that it maintains synchronization between switching and resonant frequencies, reducing losses associated with frequency misalignment. Simulation and experimental results validate the converter’s stable operation and its ability to achieve zero-voltage and zero-current switching.