The in situ microcosm experiment was set up in the four long-term fertilization field experiments, the degradation kinetics and bioaccumulation characteristics of pentachlorophenol (PCP) with initial concentration of 85 mg/kg in paddy soil-rice plant ecosystem were investigated. The long-term fertilization field experiment employed was in the Experimental Station of Red Soil, the Chinese Academy of Sciences, located in Yingtan, Jiangxi Province, China. The four long-term fertilization treatments included (1) no fertilizer (the control, CK), (2) application of urea (N), (3) application of organic fertilizer (OM), and (4) mixed organic fertilizer and urea (N OM), and no addition of PCP as control was also set up for any treatment. The results showed that carbon dioxide release in OM and N OM was both higher than that in CK, but no significant difference was observed between CK and N, indicating that long-term fertilization of organic fertilizer or mixed organic fertilizer and urea increased microbial activities in paddy soil, but no effect on microbial activity was showed under long-term fertilization of urea. PCP residue in paddy soil gradually decreased with time increasing in four treatments. After the rice plant was harvested, the final PCP residue in N OM was the least, was 8.7 mg/kg, and the highest PCP residue was in N, was 30.9 mg/kg. It could be found that PCP degradation followed one-order kinetics equation in four treatments, and the fitting degrees were 97.7%, 78.8%, 89.5%, 91.7% for CK, N, OM and N OM，respectively. According to one-order kinetics equation, the half-lives calculated of PCP degradation were 27.7, 35.2, 24.8 and 22.4 days for CK, N, OM and N OM，respectively. The results observed indicated that long-term fertilization of organic fertilizer or mixed organic fertilizer and urea accelerated PCP degradation, but long-term fertilization of urea inhibited PCP degradation. As for no addition of PCP in four treatments, the air-dried shoot and grain biomass of rice plant in N OM and OM was significantly higher than those in CK, and no significant difference was displayed between N and CK, suggesting that long-term fertilization of organic fertilizer or mixed organic fertilizer and urea increased soil fertility, but the soil fertility did not increase under long-term fertilization of urea. In the presence of PCP, the average shoot and grain biomass was remarkably smaller when compared with no addition of PCP. The average shoot biomass decreased by 40.7%, 43.9%, 58.1%, 50.6% for CK, N, OM, N OM, respectively, and 80.2%, 88.2%, 86.5%, 72.9% of grain biomass decreased was observed for CK, N, OM, N OM, respectively. It suggested that higher PCP concentration had a severe damage to rice plant aboveground part growth. Beyond understanding, the root biomass did not decrease in four treatments. No significant difference in PCP concentration in grain was observed among four treatments, the average concentration in grain was 0.51 mg/kg, and bioconcentration factors of PCP in grain were all less than 0.01. Although the half-life of PCP degradation was relatively shorter in paddy soil-rice plant ecosystem, it could be still accumulated in grain, thus posing potential food safety risk.