The present invention discloses a water head pressure control system and an apparatus for a pinhole seepage deformation test. The water head pressure control system comprises a water storage device and water supply pipes for supplying water for a seepage deformation device, wherein the water supply pipes comprise a water supply main pipe and at least a water supply branch pipe communicated with the water supply main pipe, one end of the water supply main pipe is communicated with the water storage device, the other end is communicated with each water supply branch pipe, the water supply main pipe is further provided with a water drain pipe, each water supply branch pipe end being not connected with the water supply main pipe is respectively communicated with the water inlet pipes in each seepage deformation device, the water supply main pipe is sequentially provided with a metering pump, a first accumulator, a speed regulating valve, a pressure reducing valve, a second accumulator and a pressure gauge, the water drain pipe is arranged between the first accumulator and the speed regulating valve and is provided with an overflow valve, and each water supply branch pipe is provided with a shut-off valve and a pressure gauge. According to the present invention, the structure of the apparatus is simple, the seepage deformation water pressure during the experiment process can be continuously, stably and accurately controlled, and the reliability of the experimental data can be improved.