In accordance with an embodiment, a sample analyzing apparatus includes a charged beam generating unit, a detecting unit, and an analyzing unit. The charged beam generating unit is configured to generate a charged beam and apply the charged beam to a sample. The detecting unit is configured to detect charged particles and then output a signal, the charged particles being generated from the sample by the application of the charged beam in a manner depending on a three-dimensional structure and material characteristics of the sample. The analyzing unit is configured to process the signal to analyze the sample.