The presence of diatoms in diatomaceous soil gives it geotechnical properties that are unusual compared with common clays. The most typical physical property of diatomaceous soil is its abnormally high Atterberg limits compared to fine-grained soil without diatoms. For diatomaceous soil, the Atterberg limits are associated with many factors, such as diatom content, diatom crushing degree, etc. In the study reported here, it was ascertained that more diatoms lead to higher plastic and liquid limits. Once the diatoms are crushed, the plastic and liquid limits decrease. The pore fluid salt concentration barely influenced the Atterberg limits of diatomaceous soil. Additionally, the porous diatom microstructure and trimodal pore size distribution of diatomaceous soil were investigated via scanning electron microscopy, transmission electron microscopy, and mercury intrusion porosimetry. The underlying mechanism of abnormally high liquid and plastic limits of diatomaceous soil is revealed as the water stored in the special diatom microstructure. However, water in diatoms has no contribution to plasticity. Also discussed is the applicability of the current soil classification systems for diatomaceous soil. The findings of this study can help for a better understanding of Atterberg limits of diatomaceous soil and provide suggestions for the classification of diatomaceous soil.