The original, woodland, cultivated land and lakeshore saline soil microbe of Gudahu wetland in Heilongjiang Province was selected as study object. Using the high-throughput sequencing method, we analyzed soil bacterial and fungal community structure and diversity of the four habitat types. Combining soil physicochemical index, the impact of soil environmental factor on the microbe community diversity was further analyzed. The results showed that Proteobacteria was with the highest relative abundance value in bacterial communities and Ascomycota had the highest relative abundance value in fungal communities. The bacterial community diversities were similar while the fungal were different in the same habitat; however, each of them was different in different habitats. The cultivated land soil bacterial community diversity was similar to that of woodland soil, but was closer to that of lakeshore soil. Cultivated land soil and woodland soil were with higher bacterial community diversity, followed by original soil, Lakeshore soil was with the lowest bacterial community diversity. Cultivated land soil and lakeshore soil had higher fungal community diversity, followed by original soil and woodland soil. Comparing to fungi, the diversity of bacterial community was more affected by soil environmental factors, and both pH value and moisture could significantly influence the bacterial and fungal community diversities.