The time-of-flight (TOF) mass spectrometry is one of the most widely used techniques to get information about the composition and structure of compounds. The time digitizer, based on time-to-digital conversion, is one of the important parts in modern TOF mass spectrometry, which is often implemented with analog circuitry or application-specific-integrated-circuit (ASIC) devices. However, it is difficult to achieve a high density with the analog approach. Furthermore, ASIC requires a long design cycle and the function cannot be easily revised for different applications. In this work, we present a highly flexible, accurate, yet low-costing design of time digitizer which is based on a field-programmable-gate-array (FPGA) and time interpolation method. Test results indicate that the bin size of this time digitizer is 390 ps with an average standard deviation (about 150 ps). The differential nonlinearity is in the range of -0.10 to +0.05 LSB (least significant bit), and the measurement time range is larger than 107 s. Compared with other techniques, it reduces the system complexity while providing a good flexibility. In addition, this technique can also accommodate one or more STOP pulse measurements for each START pulse reference, enabling measurement of multiple times-of-flight with a common start trigger. Besides, a time stamp is recorded for each input pulse, rendering this time digitizer versatile in other applications. Moreover, because of the programmable characteristic of a FPGA, more functions can be integrated in the time digitizer, such as a trigger function, data transfer interface; the parameters such as the number of the channels. The measurement range can also be modified according to different requirements.