Soil evaporation is a key trait in determining water consumption research of agriculture in sparse crops or in early period of the growing stages in maize and winter wheat. After measuring soil evaporation using the micro-lysimeter with different material and size in the maize and winter wheat field, we analyze the seasonal variation of soil evaporation and its variance among different micro-lysimeter material and sizes. Results showed that the seasonal maximum of soil evaporation is 6.0 and 4.6 mm/d for the maize and winter wheat, which occurs in sunny days after precipitation or irrigation when the leaf area index was small in the beginning or maturing periods. The measurements of soil evaporation using different material micro-lysimeter have no significant difference in maize field, while the large diameter micro-lysimeters measure the soil evaporation higher than the small ones. However, the different size of micro-lysimeter has no effect on the measurement of the soil evaporation in the winter wheat field. Finally, we suggest that using the micro-lysimeter with 125 mm diameter for the outer barrel in steel or plastic, 118-114 mm diameter for the inner barrel in steel in the survey of soil evaporation in Nanjing area.