Microfiltration is a promising technology for concentrating Engraulis japonicus soup by ceramic membrane. Effects of membrane pore size, pressure, temperature, initial concentration and addition modes on permeate flux were examined during microfiltration. There was no difference of the protein concentration efficiency between 0.14 μm and 0.45 μm ceramic membrane, and the integral concentration efficiency was much higher when using 0.14 μm ceramic memebrane; the permeate flux increased with temperature and pressure increased; and decreasing soup concentration could increase the permeate flux but reduced the protein concentration efficiency either. At 45 ℃,the permeate flux was higher, and the growth rate of total bacterial count and total volatile base nitrogen (TVB-N) value was minimum compared to 25 ℃ and 35 ℃, while the growth rate of thiobarbituric acid reactive substances (TBARS) value had little effect with temperature. Consequently, the optimal concentrate process was obtained under the conditions of 0.14 μm ceramic membrane, 0.3 MPa, 45 ℃ and intermittent feeding. The most effective cleaning method was 40 min at 45 ℃ with solution containing 1% (m/V) NaOH and 0.05% (m/V) SDS. The flux recovery ratio of the most effective method was 98.99%, which was 22.85% higher than that of solution only with 1% NaOH.