To solve the problems such as the difficulty of a large amount of straw returning and the slow improvement of soil fertility in barren paddy fields. Two treatments including constant application of organic fertilizer (CK: 10 t/hm2) and high dosage of pelletized organic materials deep application (POF: 40 t/hm2) were set up to study the effect of enhanced inputs of organic fertilizers (2 years) on the yield of upland rice and profile soil fertility. The results showed that high dosage of pelletized organic amendment significantly increased upland rice yield (P < 0.01), with a 24.1% increase observed in POF compared with CK. Soil bulk density increased significantly with soil depth in both CK and POF treatments. However, high dosage of pelletized organic materials deep application only improved the soil structure in the 0~20 cm, with a nonsignificant difference in other profile soils (P > 0.05). Soil organic carbon and microbial biomass decreased significantly with soil depth. Compared with CK, POF treatment only increased the contents of organic carbon content and microbial biomass in the 10~20 cm , but there was no significant difference in other profile soils (P > 0.05). Soil organic carbon, microbial biomass carbon and nitrogen in POF treatment increased by 28.2%, 70.8% and 76.1% in 10~20 cm compared with the CK, respectively. All the three soil enzyme activities including cellobiohydrolase, β-glucosidase and N-acetylglucosaminidase in the 10~20 cm increased the most than other profile soils. The random forest model analyses indicated that soil total nitrogen and cellobiohydrolase activity as key factors influencing soil organic carbon with the contributions of 10.7% and 10.0% in total soil factors, respectively. High dosage of pelletized organic materials deep application had good effects on the depth of soil ploughing layer, soil fertility and rice yields by improving profile soil structure, microbial biomass and enzyme activities in the barren paddy fields.