The major histocompatibility complex (MHC) plays a pivotal role in antigen peptide presentation and T cell immune responses against infectious disease and tumor development. The hybrid MHC I complexed with heterologous β2-microglobulin (β2m) substitution from different species can be stabilized in vitro. This is a feasible means to study MHC I of mammals, when the homologous β2m is not available. Meanwhile, it is indicated that mammalian β2m substitution does not significantly affect peptide presentation. However, there is limited summarization regarding the methodology and the technology for the hybrid MHC I complexed with heterologous β2-microglobulin (β2m). Herein, methods to evaluate the feasibility of heterologous β2m substitution in MHC I study are presented. These methods include preparation of expression constructs; purification of inclusion bodies and refolding of the MHC complex; determination of protein thermostability; crystal screening and structure determination. This study provides a recommendation for understanding function and structure of MHC I, and is also significant for T cell response evaluation during infectious disease and tumor immunotherapy.