The present invention discloses a high-precision and miniaturized on-orbit calibration device for a six-dimensional force sensor of a space station manipulator and a calibration method thereof, which include an inverted π shape fixing bracket, three force applying devices, and a cubic stress block. Each force applying device includes a force applying head, a single axis force sensor, a force source part and a fastening part. The force source part includes an upper support plate, a second electrode plate, piezoelectric ceramic plates, a first electrode plate and a lower support plate, which are coaxially arranged sequentially from top to bottom. The single axis force sensor is mounted on the top of the upper support plate, and the hemispherical force applying head is mounted on the top of the single axis force sensor. The cubic stress block is mounted on the top of the six-dimensional force sensor.