The deterioration of soil microflora and the decline of enzyme activity have been regarded as two key factors of the reduction in peanut yield in long\|term continual peanut cropping system. To understand soil biological functions in peanut cropping system, a surface layer (0-20 cm in depth) of red soil was sampled from a 15\|year\|old continuous peanut cropping upland at the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, located in Yingtan, Jiangxi province (N28°13′, E116°55′ with an altitude of 45 m ASL), and pot experiments were conducted to investigate the effects of intercropping with medicinal plants and adding endophytic fungi B3 (Phomopsis sp.) on soil microflora, saccharase, urease activities, and peanut superoxide dismutase (SOD) activity and peanut yield. The results showed that intercropping with medicinal plants and adding endophytic fungi B3 treatments significantly reduced soil mould colony forming units (CFU), but enhanced bacterium CFU and saccharase activity. The bacteria increase and mould reduction followed the order of Atractylodes lancea intercropping peanut with adding B3 treatment (PAB3) > peanut monocropping with adding B3 treatment (PB3) > Euphorbia pekinensis intercropping peanut with adding B3 treatment (PEB3) > A. lancea intercropping peanut treatment (PA) > E. pekinensis intercropping peanut treatment (PE) > control (peanut monocropping, P). Compared to the control (P), soil saccharase activity was significantly increased at flowering pegging stage in the PA and PE treatments. Its increase was greater after adding B3. The highest was observed in the PAB3 treatment combing the intercropping and B3 adding functions. Soil urease activity was also increased significantly after adding B3 (e.g., PB3, PAB3 and PEB3 treatments), although its change was less than soil saccharase activity. As a result, peanut SOD activity and peanut yield were increased significantly in the intercropping with medicinal plants and adding B3 treatments. The peanut SOD activity was the order PAB3 > PEB3 > PB3、PA > PE > P. Compared to the control (P), the PA and PE treatments rose the peanut yield by 9%-22%, while an increase of 24% was in PB3 treatment. Adding B3 increased the yield by 30% and 4% in PAB3 and PEB3 treatments than PA and PE treatments, respectively. Combining the intercropping and B3 adding increased the yield by 59% greater in the PAB3 than in the control (P), but only 13% increase was found in the PEB3 treatment. These results suggested that some synergisms might take place between the intercropping A. lancea and addition of B3 for improving peanut yield, while the presence of E. pekinensis might inhibit B3 activity to some degree, and its mechanism need more investigation.