The synchronization technology used in low-speed information protection transmission systems cannot be directly applied to high-speed information protection transmission systems. To correctly extract the ciphertext in high-speed information protection transmission systems, both communication parties must be synchronized so that the receiving end can accurately define the data transmission process, as well as the start and end positions of valid data. For a high-speed information protection transmission system encrypted using optical quantum noise, an effective key synchronization scheme is proposed herein. The synchronization frame structure and synchronization process are designed, the channel transmission delay is periodically measured, and the difference is iteratively estimated to correct the arrival time of the decryption key to complete the synchronization of the decryption key and the ciphertext under high-speed information transmission. This study analyzes the important parameters that affect the key synchronization, verifies the feasibility of the scheme, and analyzes the key performance indicators such as the success rate and bit error rate of the synchronization scheme based on the experimentally-obtained data.