Activated carbon air cathode combined with iron anode oxidation-flocculation synergistic Arsenic (As) removal was a new groundwater purification technology with low energy consumption and high efficiency for groundwater with high As concentration. The presence of organic matter such as humic acid (HA) had ambiguous effects on formation of organic colloids in the system. The effects of the particle size distribution characteristics of these colloids on the formation characteristics of flocs and the efficiency of As purification was not clear. In this work, we used five different pore size alumina filter membranes to separate mixed phase solutions and studied the corresponding changes in iron and arsenic concentrations in the presence and absence of humic acid conditions. In the presence of HA, the arsenic concentration of < 0.05 µm particle size components was 1.01, 1.28, 3.07, 7.69, 2.85 and 1.24 times of that in the absence of HA. At the same time, the arsenic content in 0.05–0.1 µm and 0.1–0.45 µm particle size components was also higher than that in the system without HA, which revealed that the presence of HA hindered the flocculation behavior of As distribution to higher particle sizes in the early stage of the reaction. The presence of HA affected the flocculation rate of iron flocs from small to large particle size fractions and it had limited effect on the behavior of large-size flocs in adsorption of As. These results provide a theoretical basis for targeted, rapid, and low consumption synergistic removal of arsenic and organic compounds in high arsenic groundwater.