【Objective】Application of organic manure or material may affect soil fertility and soil microbial community structure. However, uneven distribution of the organic materials applied in the soil may aggravate spatial heterogeneity of the soil, and hence affect structure and functions of the soil biota therein. To determine how much organic materials will affect spatial heterogeneity of the soil, an in-lab soil incubation experiment was conducted for observation of how soil protozoa and nematode community structure responded to organic materials (rice straw and white clover) in different microzones (0~1 cm, 1~5 cm). 【Method】Rice straw or white clover was proportionally mixed up with soil and put into net bags separately. Then the bags were put into the vessels of the tested soil, separately, for incubation under a constant temperature (25±1℃) for 70 days. Soil samples were collected from microzones adjacent to (0~1 cm) and far apart (1~5 cm) from the net bags, on D14, D35 and D70 for analysis of abundance, Shannon-Wiener index (H' ), structure index (SI) and maturity index (∑MI2-5) of nematodes, and soil dissolved organic carbon (DOC), dissolved organic nitrogen (DON), nitrate nitrogen (NO₃⁻-N), microbial biomass carbon (MBC) and nitrogen (MBN), as well, which may be related to changes in the microfauna in the soils amended with rice straw or clove. 【Result】In this experiment, it was found that on the whole kind of the organic material and duration of incubation were the two major factors affecting the numbers of protozoa and nematodes, however, it does not mean that location of the microzone for sampling had no impact on soil microbes therein. Within the initial period of incubation (0~14 days), in microzones of the soil amended with the same organic material, the numbers of soil microbes in the adjacent microzones (0~1 cm) were higher than those in the far-apart microzones (1~5 cm), which is more obvious in the soil added with white clover. With the incubation going on (14~70 days), relative abundances of plant-feeding and fungi-feeding nematodes were higher in the soil added with rice straw than those in the soil added with white clover, whereas relative abundances of soil amoeba, flagellates, total nematodes and bacteria-feeding nematodes went reversely. Different kind of organic material also triggered different changes in Shannon-Wiener indices, structure indices and maturity index of nematodes. Shannon-Wiener index and structure index in adjacent microzones were found higher than those in far-apart microzones in the soil added with white clover, however the disparity was not found in the soil added with rice straw. The number of flagellates decreased, while the numbers of amoeba and nematodes increased with the incubation going on. 【Conclusion】Therefore, it is quite obvious that during the initial period of incubation, distance of microzones from the net bag of soil does have some influences on both the numbers of protozoa and nematodes, especially nematodes, and dthe influence fades with the incubation going on, while, the difference in type of organic material is the factor eventually affecting abundance and community structures of the nematodes.