In order to study the ecological effect of balanced fertilization on paddy soil with P-deficiency treated, a pot-experiment by cropping rice had been conducted for 3.5 years. The soil for experiment was got from the plowed layer soil in plot treated with chemical N and K but P-fertilizer in a long-term experiment of soil fertility and benefit of fertilizer in red earth paddy soil. Six different treatments including chemical N and K (NK), N, P, and K chemical fertilizer (NPK), N, P, and K chemical fertilizer mixed with Si fertilizer (NPKSi), three-fifths of N, P and K chemical fertilizer and two-fifths of organic manure (NPKM), increasing P chemical fertilizer based on NPK (NKhP), and increasing P chemical fertilizer based on NPKM (NKhPM) were examined. The chemical fertilizer N, P, K, Si for experiment was urea, calcium magnesium phosphate, potassium chloride, and sodium silicate, respectively. The organic manure when cropping early rice was Astragali and pig feces, and when late rice was green straw of rice and pig feces. All fertilizers applied to soil with once application as base fertilizers. When the rice was harvested, soil samples were collected for measuring soil fertility and microbial characteristics; the samples of rice were also collected in the stages of rice maximum tillering, heading, and harvesting, respectively, for the rice biomass and the nutrient quantity; the samples of leaching water were collected after fertilization 1 day, 3 days, 7 days, 15 days, 30 days, 45 days, 60 days and on the day when rice harvested, respectively, for the content of total P. Every treatment was replicated for 6 times. The experiment was carried out in a greenhouse. The cropping system was as rice-rice-fallowing. The indexes of soil fertility, soil microbial characteristics, the content of total P in leaching water, grain yield, nutrient use efficiency and agricultural P fertilizer use efficiency for each treatment were measured/calculated and compared. The results showed that balanced fertilization treatments of NPK, NPKSi, NPKM and NKhPM significantly enhanced the averaged rice yield (147% higher than NK, and NPKM was 152% higher), the indexes of soil fertility (18.5% higher content of organic matter in soil than NK, and NPKM was 30.1% higher), the microbial biomass (57.1% content of MBC higher than NK, and NPKM was 87.1% higher), the nitrogen use efficiency (120.3% higher in IEN than NK, and NPKM was 152% higher), and the potassium use efficiency (33.6% higher than NK, and NPKM was 43% higher). However, although NKhP reached a high rice yield which was 125.1% higher than NK, its soil microbial activity and MBC were 9.4% and 2.4% lower than NK, respectively, mainly due to higher content of phosphate that led the microbe community to grow unhealthy in paddy soil. As results, its quality of paddy soil microbial ecosystem grew worse. Furthermore, excessive application of P-fertilizer (included of NKhP and NKhPM) led to water pollution from phosphorous in rice field. In conclusion, the treatment of NPKM had the best ecological effects under all of treatments, followed by NKhPM, NPKSi, NPK and NKhP that produced negative effect on microbial ecosystem in paddy soil. Accordingly, balanced fertilization was the effective method to restore the paddy soil with P-deficiency, and the treatments of adding organic manure or Si-fertilizer based on balanced application of N, P and K fertilizer had a better effect.