High precision timing distribution is crucial to many large scale cosmology and particle physics experiments. Besides the space and energy information, the accurate timing provides an extra dimension for physics event reconstruction. In the timing distribution system, accurate clock phase measurement is an indispensable tool to monitor the phase drift and to achieve accurate phase adjustment. This paper introduces a novel phase measurement method implemented in the Xilinx Field Programmable Gate Array (FPGA). It uses the dedicated phase interpolator in the multi-gigabit transceiver. A design based on this method is implemented within the Kintex Ultrascale series FPGA. The preliminary test result shows that a sub-picosecond level precision is achieved. With this system, the nonlinearity of the phase adjustment in the Xilinx transceiver is measured.