Provided is a substrate contamination analysis system capable of individually analyzing impurities present in a film and impurities present on a surface of the film. The substrate contamination analysis system includes: a vapor phase decomposition device configured to expose a film formed on a surface of a first substrate to a gas that reacts with the film, to thereby dissolve the film; a recovery device configured to perform a first recovery operation of moving an object to be measured to a first measurement position before the film is dissolved and a second recovery operation of moving the object to be measured to a second measurement position after the film is dissolved; and an analyzer configured to analyze the object to be measured every time the recovery device performs the first recovery operation and the second recovery operation.