The invention discloses a vehicle-mounted weighing system of a freight train as well as a weighing method. The weighing system comprises a weighing sensor, a connecting cable and a vehicle-mounted intelligent terminal, wherein the vehicle-mounted intelligent terminal consists of an ARM embedded controller unit, a power supply unit, a positioning unit, a wireless data transmission unit, a digital I/O interface unit, a weighing signal amplifying and conditioning circuit, an analog-digital conversion circuit and a data storage unit. A bogie strain-based indirect type weighing method is adopted bycombining the own structure of a rail wagon. For the safe working characteristic of railway freight, the weight of the wagon is monitored in real time in the loading, transportation and unloading processes of the freight train, and whole-course dynamic weighing of the whole wagon and the whole route is realized. The vehicle-mounted weighing system has remote monitoring and failure diagnosis functions, is high in measuring result precision and stability, has the characteristics of reliable performance, low cost of monitoring equipment and low requirements on mounting and use conditions, and iseasy to popularize and use.