A new strategy is proposed based on inhibition of ion transport by lipid bilayer derived from spontaneous assembly of lipopolysaccharides (LPS), thereby a colorimetric method is established for analysis of LPS. At acidic pH values, LPS can specially bind with aminophenylboronic acid modified assembled magnetic nanospheres (APBA/AMNSs), resulting in formation of lipid bilayer around APBA/AMNSs. Under acidic condition, the lipid bilayer can inhibit the release of iron ions from AMNSs into the solution so as to decrease the oxidized extent of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt mediated by hydrogen peroxide. Using the established method, LPS can be detected over the wide linear detection range with the low detection limit. With good selectivity, reproductivity, and simplicity, the method is accurate in LPS tests of real drinking samples.