The invention discloses a passenger identity verifying security-checking system and an operation method thereof. The security-checking system structurally comprises a security-checking door, passage guardrails and a speedy through door, wherein the speedy through door comprises a left side gate and a right side gate; the security-checking door and the speedy through door are connected with each other through the passage guardrails; the upper part of an inside door frame of the security-checking door is provided with a site videoing camera; the end surface of an upper cover of a box body of the left side gate is provided with a second information prompting screen and a radio frequency card reader; the end surface of an upper cover of a box body of the right side gate is provided with a touch screen, a certificate scanner and a portrait acquisition camera; the inclined side surface of the upper cover of the box body of the right side gate is provided with a first information prompting screen and a certificate card reader; the upper part of one side surface of the box body of the right side gate is provided with a passage state indicating screen; the box body of the right side gate is internally provided with a small-sized industrial personal computer. The security-checking system has the advantages of being convenient and practical and can be used for acquiring the identity information of passengers or visitors and checking the security of articles carried with the passengers or the visitors.