The invention relates to a flue gas sampling system for a gas boiler. At least two sampling ports are included, and during sampling, the sampling ports are vertically distributed in the direction vertical to the flue gas flowing direction at intervals on the cross section of a flue channel; sampling pipelines and the sampling ports are formed in a one-to-one correspondence manner, the first end ofeach sampling pipeline is connected with the corresponding sampling port, and a first switch valve is arranged on each sampling pipeline; a sampling tube is communicated with the second end of each sampling pipeline respectively, and an outlet pipe stretches out of the sampling tube, and the outlet pipe is used for being connected with a flue gas analyzer. According to the flue gas sampling system, the equipment cost is reduced, the pipeline maintenance of equipment is facilitated, the equipment cost is reduced, the sampling time is shortened, and the flue gas sampling efficiency is improved.The invention also discloses a flue gas sampling method of the gas boiler.