A method and apparatus for measuring endogenous CO concentration in exhaled alveolar air, comprises: proposing a method for injecting samples in small amounts, multiple times, intermittently, and establishing a CO concentration relationship between sample gas and gas in a measuring chamber; establishing a “concentration difference/electrical level difference” difference value fitting method, to obtain a fitted standard curve for a difference value between the sample gas and base gas; establishing an apparatus for measuring a CO concentration difference and a CO2 concentration difference between sample gas and base gas; proposing a method for compensating a measurement value for endogenous CO in exhaled alveolar air. The problem that the amount of sample gas in a breath test is small, and cannot completely replace the gas originally inside the measuring chamber, is solved. The effect of electrical level zero drift and residual CO of unknown concentration in cleaning gas is eliminated.