A data synchronization system includes a first memory device in a handheld electronic device, a second memory device in a desktop computer, and a synchronization program installed in the desktop computer. The handheld electronic device includes a first data block. The desktop computer includes a second data block. First and second data formats of first and second data stored in the first and second data blocks respectively include a common format section. The first and second memory devices store first and second modification records of the first and second data blocks, respectively. The synchronization program updates the first and second data blocks according to the first and second modification records and transmits only the contents of the common format section when transmitting the first or second data between the handheld electronic device and the desktop computer. A data synchronization method implemented in the system is also disclosed.