Data acquisition based on network-on-chip (NoC) technology is a high-sampling-rate data acquisition scheme using low-sampling-rate analog–digital conversion (ADC) chips. It has the characteristics of multi-task parallel communication, being global asynchronous, local synchronous clock distribution, high throughput, low transmission latency, and strong scalability. High-speed data acquisition is realized through the combination of an on-chip network and time-interleaved data acquisition technology. In the time-interleaved sampling technique, the precision of clock synchronization directly affects the precision of sampling. Based on the proposed NOC data acquisition scheme, an improved White Rabbit clock synchronization protocol is applied to high-speed data acquisition to achieve high-precision synchronization of multi-channel time-interleaved sampling clocks. Firstly, the offset of the master clock and slave clock is determined by the PTP protocol, and the offset is corrected to achieve rough synchronization between the master clock and slave clock. Secondly, a digital dual-mixer time difference (DDMTD) is used to measure the phases of the master and slave clocks. After that, the phase of the slave clock is corrected through the dynamic phase-shift function of the clock’s phase-locked loop (PLL). Finally, according to the simulation results in Modelsim, the average absolute error of a TI-ADC sampling clock can be less than 20 ps.