The invention discloses a two-stage power converter adopting a lightning protection design and a system. The two-stage power converter comprises multiple former-stage power conversion units and a latter-stage power conversion unit, wherein input of each former-stage power conversion unit is independent, and output of each former-stage power conversion unit is connected in parallel to the latter-stage power conversion unit; each former-stage power conversion unit specifically is a three-level Boost circuit provided with a bypass diode; besides, each former-stage power conversion unit is provided with a Y-type lightning protection circuit connected between an input positive electrode and an output negative electrode of the former-stage power conversion unit and the ground and formed by a lightning arrester; and at least two Y-type lightning protection circuits are grounded through the common lightning arrester to increase impedance of a line through which Ib flows, and Ib is lightning stroke current shunt flowing to a bus capacitor. Failure of bypass diodes in the former-stage power conversion units is avoided.