The availability of continuous and well-defined AFI-type aluminophosphate membranes (AFI membranes) would trigger their applications in innovative materials. A well-designed manipulation strategy is proposed to produce continuous AFI membranes with four different microstructures over porous α-Al2O3 substrates. A double-layer and highly c-oriented AFI membrane of hexagonal prisms is obtained when a thin layer of medium molecular weight (MMW) chitosan is employed as the structure-directing matrix together with aluminum isopropoxide (AIP) as the Al source. It can be transformed to a single-layer and highly c-oriented AFI membrane of hexagonal prisms if the structure-directing matrix is replaced by a thin layer of low molecular weight (LMW) chitosan. When the Al source is changed to pseudo-boehmite, the single-layer AFI membrane is composed of highly ordered spherical agglomerates of small crystals. Furthermore, the membrane will turn to the double-layer AFI membrane of highly-ordered crystal agglomerates if a thin layer of MMW chitosan is used once again, keeping pseudo-boehmite as the Al source. The manipulation methodology established here is rather reliable with a pretty high reproducibility.