At present, farmland-controlled drainage is of great significance for water-logging control, water conservation, and emissions reduction. This paper focused on the water level of farmland to study the changes of root-zone soil environment in a flooded paddy field. Such technical indexes included the soil nutrient index of rapid available phosphorus (RAP) and rapid available nitrogen (RAN) in the 0-10 cm and 10-20 cm soil layers, the soil aeration condition index Eh value in the 15 cm soil layer, and soil temperature (ST), respectively, in the 5 cm and 20 cm soil layers. Additionally, this paper presented an analysis on the impact of water flooding in a paddy field on the soil’s microenvironment using the principal component factor method. Influence analysis results showed that different water level controls between CK (shallow and wetting irrigation) and F1 and F2 (controlled drainage) had a significant effect on the changes of RAN content in the 0-10cm layer, Eh value in the 15 cm layer, and ST value in the 5 cm layer, but different leakage intensities had no significant effect on the change of RAN, RAP, Eh, and ST. The results showed that water-flooding can improve the RAP content, reduce the RAN content of every soil layer, deteriorate the soil aeration status, and increase the soil temperature; additionally, the water-flooding had an adverse impact on the soil’s RAP, RAN, Eh, and ST at the tillering and milking stages. Water-flooding also had an adverse impact on the soil’s RAN and Eh at the jointing-booting and heading-flowering stages.