The invention discloses a clock synchronization device and a base station system. The device comprises a microcontroller, a digital to analog converter, a constant temperature crystal oscillator, a comparer and an IRIG-B (Inter Range Instrumentation Group) coder/decoder. The IRIG-B coder/decoder comprises a decoding input interface, a decoding output interface, a coding input interface and a coding output interface. The input end of the digital to analog converter is connected with the output interface of the microcontroller and the output end is connected with the input end of the constant temperature crystal oscillator. The output end of the constant temperature crystal oscillator is connected with the first input end of the comparer and the coding input interface. The second input end of the comparer is connected with the decoding output interface. The result output end of the comparer is connected with the input interface of the microcontroller. The clock synchronization device and the base station system are good in compatibility.