The present disclosure provides a sample analyzer and an analyzing method thereof. The sample analyzer includes a first beam source configured to provide a first energy beam to a sample, a second beam source configured to provide a second energy beam, which is different from the first energy beam, to the sample, a reflected beam sensor disposed between the second beam source and the sample to detect a reflected beam of the second energy beam, which is reflected by one side of the sample, and a transmitted beam sensor disposed adjacent to the other side of the sample to detect a transmitted beam of the second energy beam.