Long-term application of chemical fertilizers has aggravated red soil acidification and caused severe early defoliation in pear-growing region of southern China. To investigate the effects of BIO and HA on the growth and activity of fine roots, and in turn the effect on leaf nutrient status and early defoliation of pear trees, we conducted a 2-year pot experiment (2018–2019) using 1-year-old pear (Pyrus pyrifolia) seedlings in a pear orchard in southern China. Four fertilization treatments were included: chemical fertilizer as control (CF), CF with humic acid (CF-HA), BIO, and BIO mixed with HA (BIO-HA). Results showed that BIO and BIO-HA treatments significantly decreased the early defoliation rate of pear trees about 18%–27% compared with CF and CF-HA treatments. For the growth status of the aboveground, the relative growth rate of pear trees treated by BIO and BIO-HA was 1.2 times higher than the CF treatment at 180 days after budding, and it was accompanied by an increase of leaf thickness, microelements content (e.g. calcium, manganese, iron and zinc), and a decrease of leaf temperature. Compared with CF treatment, BIO or BIO-HA significantly improved soil pH value by 0.9–1.1 units, and increased soil exchangeable calcium content by 50%–83%. BIO and BIO-HA treatments also significantly increased total lateral root number, length and root activity, which were negatively correlated with the early defoliation rate by the network analysis. Furthermore, structural equation model showed that root traits were the core factor to alleviate the early defoliation rate, which was directly or indirectly driven by the application of bioorganic fertilizer. In conclusion, BIO or BIO combined with HA can alleviate the early defoliation rate of pear trees by mitigating soil acidification to stimulate the lateral root growth and activity, and in turn increase leaf micronutrients content and aboveground growth. Our study shows that measuring root traits are at the core of plant responses to soil nutrient status and pH.