Based on 6-years irrigation experiment in greenhouse, micro-scale spatial variability and the distribution of surface soil pH were analyzed by combining classical statistic method with geostatistic method with a small grid-sampling technique under three irrigation methods (furrow irrigation, drip irrigation and subsurface irrigation). The results indicated that, after 6-years irrigation, soil pH under furrow irrigation decreased significantly, soil pH (0 ~ 5 cm) under furrow irrigation and drip irrigation were medium heterogeneity, and soil pH (5 ~ 10 cm) of furrow irrigation and drip irrigation, soil pH (0 ~ 5, 5 ~ 10 cm) of subsurface irrigation which were weak heterogeneity. The supplying way and quantity of water by irrigation can affect the spatial variability of soil pH.