The invention relates to a pile foundation underpinning system based on a double-layer permanent lining structure and a construction method of the pile foundation underpinning system. Affected by thesurrounding environment and traffic, when a tunnel passes through an existing pile foundation, a conventional simply supported beam-pile underpinning system may not have an implementation condition. The pile foundation underpinning system comprises the double-layer permanent lining structure composed of the two parts of an outer side underpinning lining and an internal tunnel lining. The underpinning lining is applied to the position between the tunnel lining and the existing pile foundation, the bottom of the existing pile foundation extends into the underpinning lining and an underpinning joint is formed, and effective connection of the joint is achieved by utilizing steel bar embedding and steel bar mechanical anchoring. According to the pile foundation underpinning system based on thedouble-layer permanent lining structure and the construction method of the pile foundation underpinning system, effective transmitting and structural underpinning of a pile foundation load are achieved, the construction negative influences caused by the fact that the tunnel passes through the existing pile foundation are reduced to the utmost extent, the pile foundation underpinning system has theadvantages of being good in settlement control and safe and reliable in underpinning system, the defects that construction of the conventional beam-pile underpinning system has a large influence on the environment and is high in construction cost, complex in stressed system and the like are overcome, and the blank that domestic and overseas bridge pile foundations adopt tunnel lining underpinningis filled up.