"The interface is the device," a famous phrase coined by Nobel laureate Herbert Kroemer, has highlighted the importance of materials interfaces for the functionalities and performance of electronic devices. Semiconductor:dielectric interfaces play central roles in transistors: one of the main reasons of the success of silicon technology and the bottlenecks of many proposed alternatives, among which are the 2D transistors. Major 2D semiconductors, such as MoS2, WSe2, HfSe2, and ZrSe2, have not yet given rise to workable devices based on native high‐K stacks by thermal oxidation which is highly technologically desired. Recently, this feasibility has been demonstrated in Bi2O2Se, an emerging layered 2D material, with its native high‐K oxide, Bi2O5Se. Understanding the atomic‐scale properties of the Bi2O2Se:Bi2O5Se interface is crucial for the developmental applications of this emerging 2D analogue of Si:SiO2. Herein, the atomic structures and band alignment properties of various Bi2O2Se:Bi2O5Se interfaces with different configurations of the interfacial anion layers are comprehensively studied. The correlation between band offset and interfacial atom intermixing is observed and rationalized. The interfacial anion vacancies are also investigated and it is found that oxygen vacancies are detrimental.