CryoEM single particle reconstruction technique is a widely used method for solving macromolecular structures in structural biology. However, there are still some shortcomings in the current processes of single particle three-dimensional reconstruction. None of the current single particle reconstruction software has implemented the function of automatically finding soft mask for binary mapping out the reconstructed map, which can import bias in the computation of statistical model of noise, influencing effectiveness of three-dimensional reconstruction. To solve this problem and to improve the solvent flattening operation in single particle reconstruction, here, we report a new method for automatically finding soft mask for mapping out the reconstructed map in single particle reconstruction, by using Gaussian filtering, Canny edge detection, minimum error thresholding etc., for processing reconstructed map. This new method is derived from the solvent flattening method, which is widely used in X-ray crystallography for solving and improving macromolecular phases. In the experiment, we implemented FSC between reconstructed maps, Euler angular error scatter plot etc. methods to assess effect of auto-mask method. It was shown that mask map generated by auto-mask method can soundly cover molecular signal region of reconstructed map, and our new auto-mask method in three-dimensional reconstruction can help to improve resolution of three-dimensional reconstruction.