To explore the long-term effects of biochar on growth promotion and soil nutrients of the intercropping system of Machilus pauhoi and Ilex latifolia, a field plot experiment was carried out to study the growth dynamics of M. pauhoi and inter-annual variability of soil nutrient content from 2015 to 2017 under the treatment of four biochars of 0 (CK), 1.2 (T1), 2.4 (T2), and 4.8 kg (T3). The results showed that the M. pauhoi growth rate was slow in the early stage, but accelerated after transplantation at 16 months. Biochar promoted the height, leaf length, and leaf width growth of M. pauhoi, but there was no significant difference between the different dosages. Compared with the control, the shoot dry weight of M. pauhoi under T1, T2, and T3 treatments increased by 35.71%, 59.02% and 31.81% respectively, whereas the root dry weight increased by 28.02%, 39.69%, and 20.52% respectively. The soil pH, organic matter, and available potassium content in 0-15 and 15-30 cm soil layers increased with biochar application rates over three years. After biochar application, the content of total nitrogen, phosphorus, and potassium in the soil increased slightly. The alkali hydrolysable nitrogen content in the 0-15 cm soil layer decreased in 2015 and 2016, but increased in 2017 and the increment effect was not significant (P > 0.05). There was no obvious change in alkali hydrolysable nitrogen content in the 15-30 cm soil layer. The change in available phosphorus content in the 0-15 cm soil layer in 2015 was not obvious after biochar application, but it increased in 2016 and 2017. In addition, the effect of T1 and T3 treatments were the most significant. Biochar increased the available phosphorus content in the 15-30 cm soil layer, but it was not significant later (year 2017) (P > 0.05). In general, the trend of the soil nutrient content under each treatment was: 0-15 > 15-30 cm, year 2015 > 2016 > 2017. There was a significant positive correlation between M. pauhoi biomass and the 0-15cm soil nutrient content, and different soil nutrient contents. With respect to biochar application, the effect of T2 was most pronounced with regard to promoting growth and holding fertilizer and was also long lasting.