GNSS reference stations are vulnerable to the thunders and lightning. The design of lightning protection devices is of great importance for the establishment of GNSS reference stations. According to the regulations of lightning protection for general buildings and the characteristics of GNSS reference stations, the lightning protection levels of GNSS reference stations are analyzed, and the external and internal protection of lightning arresters, down conductors, grounding, equipotential bonding, shield, reasonable wiring and SPDs are discussed. Practice shows that the method is effective for preventing the reference stations from being stricken by lightning.