A charged particle beam system for measuring a sample such as a photomask is provided. The system is capable of adjusting its condition with high accuracy to measure the sample even when a back surface of the sample is charged. The charged particle beam system measures an electric potential distribution on the back surface of the sample during a process for transporting the sample. The system controls the degree of charge neutralization of the sample based on the result of the measurement, or estimates or calculates an electric potential distribution appearing on a front surface of the sample and obtained when the sample is placed on the sample holder or the like. The system is capable of measuring or inspecting the sample such as a photomask at high speed and with high accuracy even when the sample has a large amount of charges accumulated on its surface different from its pattern surface.