Pulsed electric fields (PEF) were applied to neutral ginkgo cloudy juice to study the influence of the electric field strength, the treatment time and temperature on microbial inactivation. The results showed that microbial inactivation increased with the electric field strength, the treatment time and temperature. PEF treatment caused 3.39 and 4.44-log cycles reduction of coliforms and total plate counts, respectively, when pulse duration was 3 μs, the electric field strength 30 kV/cm, the treatment time 520 μs and the water bath temperature 15°C. Under the same conditions, the microbial shelf life of ginkgo cloudy juice was extended to 24 days at 4°C and 18 days at room temperature. A 3.7-log cycles reduction of the total yeast and mould counts was obtained by applying 390 μs of 30 kV/cm at 15°C.Yeast and mould cells were less resistant to PEF process than bacteria cells. The effect of heat generated during the PEF treatment was limited on microbial inactivation. Temperature and the induced heat by PEF had synergistic effects to microbial inactivation in cloudy ginkgo juice.