The invention relates to a timing running second chronograph clock mechanism and a working method thereof. The timing running second chronograph clock mechanism is characterized by comprising a control circuit, a traveling time gear, a running second gear, a scoring gear and a second stopping timing mechanism, wherein the control circuit is used for controlling each motor output; the second stopping timing mechanism comprises a main clamping plate and a minute gear component, a minute gear, a handle shaft, a clutch rod and a second stopping column which are arranged on the main clamping plate; the clutch rod is arranged as an arc-shaped warped rod; a rotating hole is formed in the clutch rod; a positioning shaft matched with the rotating hole of the clutch rod is arranged on the main clamping plate; one end of the clutch rod, close to the rotating hole, is arranged as a head end; a support arm being separated from or in contact with the handle shaft is arranged at the head end; one end of the clutch rod, away from the rotating hole, is arranged as a tail end; the tail end is resisted against the second stopping column all the time. Compared with the prior art, the timing running second chronograph clock mechanism has the advantages of contact and separation reliability and difficulty in deforming the clutch rod.