The invention discloses a vehicle starting protecting system and a control method thereof. A starting protecting controller in the system is electrically connected with an electric quantity sensor, an environment temperature sensor, an ignition switch position collecting module, a clutch opening degree collecting module and a shift lever position collecting module respectively to be used for judging whether a quasi-starting condition is met according to the remaining capacity of a storage battery and environment temperature when an ignition switch gear is an ON gear, the starting protecting controller is also used for judging whether a starting condition is met according to the clutch opening degree and the gear shifting position when the quasi-starting condition is met and the ignition switch gear is a starting gear, and when the starting condition is met, a coil of a starting cut-out relay is controlled to obtain electricity, so that an engine is started. Whether the engine is suitable for being started currently is judged according to the remaining capacity of the storage battery and environment temperature first, then under the condition proper for starting, whether the starting condition is met is judged according to the gear shifting position and the clutch opening degree, the safety of a starting process is guaranteed, and driving safety is improved.