An embodiment of the invention discloses a measurement system and method for transient voltage in transformer windings. The system is characterized in that a transformer comprises a transformer housing, the upper portion of the transformer housing is a cone, a transformer core and transformer windings are disposed inside the lower portion of the transformer housing, and the whole transformer housing is grounded; one end of each transformer winding is grounded, the other end of every transformer winding is connected with a high-voltage nanosecond square wave source sequentially through a variable impedance transmission wire and a coaxial transmission wire, and the variable impedance transmission wire comprises a conical part on the upper portion of the transformer housing and a conical high-voltage lead inside the conical part; the parts of the transformer housing, corresponding to the transformer windings, are provided with a plurality of capacitance sensors forming a distributed capacitance sensor array; the capacitance sensors are connected with a signal processing and storage unit through signal transmission cables. The system and method has the advantages that nanosecond square-wave voltage can be loaded to the transformer windings in an undistorted manner and the measurement sensors have no effect on transformer winding distribution parameters and winding transient voltage distribution.