Phenomena of communication outage, installation’s power source damage and equipment function disorder caused by thunder and lightning every year appeared in microcomputer protection, background monitor and network communication of 110 kv electric substation in inclined trench mine. Meanwhile, potential risk of background monitor and prevention loss existed in electrical equipment of electric substation. Based on this condition and analysis of site operating environment together with existing ground conditions, reason of substation secondary system influenced by thunder and lightning was explored and lightning protection alteration goal was put forward. As a result, comprehensive reconstruction scheme containing secondary system laying low resistance, corrosion of grounding network independently and level 3 power lightning protection device setting was adopted. The practice showed that prevention loss of substation secondary system and power supplies were improved remarkably, which acknowledged this scheme firmly.