The high accuracy time synchronization signal based on global positioning system（GPS） is widely used in many fields like wide area measurement system（WAMS）， but in actual applications some problems such as losing satellite lock will lead to synchronous clock signals getting out of sync. A high accuracy time keeping scheme by presetting time difference compensation is proposed. A high accuracy time keeping GPS timing system prototype based on GPS receiver and complex programmable logic device（CPLD） is developed. Comparative tests are made between the time keeping scheme proposed and the other two time keeping schemes， i.e. rising-edge time synchronization scheme and time difference feedback adjusting scheme. Test results show that when using the time keeping scheme proposed， the PPS（pulse per second）signal reaches an accuracy of±300 ns under normal conditions and will ensure an accuracy of±20μs when losing satellite lock within 24 hours， which is obviously better than the other two schemes.