In order to achieve the remote reference measurement in the seabed magnetotelluric data acquisition, every instrument needs to collect the data synchronously. Therefore, the precision and stability of the clock become the key link in keeping normal operation of the equipment. The authors designed a highly precise clock module with the error margin only at the microsecond level, which uses the microcontroller as its main control unit and employs such techniques as serial communication and I2C. This paper mainly describes the hardware and software design of the clock.