Abstract: Aspergillus niger is an important microorganism in biotechnology and its metabolites play an important role in fermenting feed, food ingredients, enzymatic production and medicine; it is known as a cell-production plant for heterologous proteins and enzymes. Glucoamylase produced by Aspergillus niger is widely used to hydrolyze starch into glucose in brewery industry, calcium lactate industry and a variety of fermentation industry; it is regarded as a generally safe product by food and drug administrations. Although glucoamylase produced by Aspergillus niger has been studied for many years, there is still room for improvement such as enhancing glucoamylase activity, reducing energy and production costs. As such, Aspergillus niger still attracts research interest. Compared with chemical mutation and recombination technology, the pulsed electric field is able to improve microbial activity and its fermentation ability with limited chemical residues and short cultivation period. In this work, we cultured and processed aspergillus niger spore suspension under different pulsed electric field in attempts to understand the responsive changes in its biological activities and glucoamylase production. The pulsed electric fields we examined had pulse intensity: 5-15 kV/cm, pulse duration: 10-100 s and pulse numbers: 50-99, and they were compared to the surface method. The results showed that both pulse intensity and pulse number affected the dry weight of Aspergillus niger mycelium and the production of glucoamylase. When the pulse intensity and pulse width were 12.975 kV/cm and 54 μs, respectively, and the pulse number was 66, the dry weight of Aspergillus niger mycelium was 28.05 mg and the productivity of the glucoamylase was 18.01 U/mL, increasing by 68.27% and 14.71% respectively up the control. Compared with clear colony circles of untreated colonies, the colonies processed by the PEF was round while the colony circles were hardly distinguishable from the star-shaped folds and higher colony circles. The PEF treatment significantly increased the spore number, with a distinct dark yellow appearing around the spores while the color of the spores remained unchanged. The observed colony morphology showed that the PEF treatment boosted the growth of Aspergillus niger due to the change in its metabolism. Statistical analysis showed that PEF treatment improved the spore germination rate by 77.8%-231%, thereby promoting mycelial growth. Esterase isozyme analysis showed that PEF treatment altered the brightness and width of the bands but not the band number. It was also found that the PEF treatment affected the enzymatic activity in all experiments although it did not have significant effects on genetic mutagen. This work provides a theoretical basis to improving enzyme synthesis of Aspergillus niger and its industrial production.