In lots of reports, improvement of shale percolation ability by shale-hydration has been reported, some researchers even regard low hydraulic fluid flowback rate as an advantage; they mainly focused on inorganic pores and fractures because brittleness of inorganic minerals decides the fracturing effects, but organic pores occupy large proportion of shale pores. In order to discover the moisture influence on organic pores, we prepare 4 samples by adjusting water content reaching 9.37%, 35.97%, 61.6%, and 80.45% and observe and quantitatively analyze 10,343 pore changes before and after processing of the 4 samples through SEM and image processing software, respectively, meanwhile, match the incremental water invasion rate curve with the dry pore size distribution curve. We also compare the water invasion mass of normal shale sample and organic partially removed sample. This paper first visually observes and counts the influence of hydration on organic shale pores through analysis of pore number, diameter, kurtosis, median, area, and characteristic lengths; discovers hydration and dehydration jointly cause the expected changes; the whole procedure contains two opposite mechanisms, pore closure or deformation caused by squeeze and enlarged pores or newborn fractures caused by water flush. Based on experimental and analysis results, conclusions are drawn that organic pores can be influenced by moisture, water flush and clay hydration expansion work jointly, and water flush function is weak when moisture is low, but it becomes stronger with the sufficient moisture. Therefore, sufficient soak time is beneficial to development.