Abstract It is well known that the traditional two-dimensional electron system (2DES) hosted by the SrTiO₃ substrate can exhibit diverse electronic states by modifying the capping layer in heterostructures. However, such capping layer engineering is less studied in the SrTiO₃-layer-carried 2DES (or bilayer 2DES), which is different from the traditional one on transport properties but more applicable to the thin-film devices. Here, several SrTiO₃ bilayers are fabricated by growing various crystalline and amorphous oxide capping layers on the epitaxial SrTiO₃ layers. For the crystalline bilayer 2DES, the monotonical reduction on the interfacial conductance, as well as carrier mobility, is recorded on increasing the lattice mismatch between the capping layers and epitaxial SrTiO₃ layer. The mobility edge raised by the interfacial disorders is highlighted in the crystalline bilayer 2DES. On the other hand, when increasing the concentration of Al with high oxygen affinity in the capping layer, the amorphous bilayer 2DES becomes more conductive accompanied by the enhanced carrier mobility but almost constant carrier density. This observation cannot be explained by the simple redox-reaction model, and the interfacial charge screening and band bending need to be considered. Moreover, when the capping oxide layers have the same chemical composition but with different forms, the crystalline 2DES with a large lattice mismatch is more insulating than its amorphous counterpart, and vice versa. Our results shed some light on understanding the different dominant role in forming the bilayer 2DES using crystalline and amorphous oxide capping layer, which may be applicable in designing other functional oxide interfaces.