As a key step in secondary refining, the deoxidation process in clean stainless steel production is widely researched by many scholars. In this study, vacuum oxygen decarburization (VOD) deoxidation refining in a 40-t electric arc furnace + VOD + ingot casting process was analyzed and optimized on the basis of Al deoxidation of stainless steel and thermodynamic equilibrium reactions between the slag and steel. Under good stirring conditions in VOD, the deoxidation reaction reaches equilibrium rapidly, and the oxygen activity in the bulk steel is controlled by the slag composition and Al content. A basicity of 3–5 and an Al content greater than 0.015wt% in the melt resulted in an oxygen content less than 0.0006wt%. In addition, the dissolved oxygen content decreased slightly when the Al content in the steel was greater than 0.02wt%. Because of the equilibrium of the Si–O reaction between the slag and steel, the activity of SiO₂ will increase while the Si content increases; thus, the Si content should be lowered to enable the formation of a high-basicity slag. A high-basicity, low-Al₂O₃ slag and an increased Si content will reduce the Al consumption caused by SiO₂ reduction.