To observe and understand subcellular structures of cells, cryo soft X‐ray imaging is a promising and effective method. For identification of organelles inside the cell, different auxiliary imaging modalities are usually required, such as fluorescence microscopy, which will increase work and introduce toxicity to biological sample. In this work, absorption properties of soft X‐rays was used to identify the organelles inside the cell, because the absorption of soft X‐ray is an inherent property of substances. Quantitative analyses of the identified organelles of different cells were also carried out. The specific process methods as well as the experimental conditions are described in detail.