Tolerance　allocation　optimization　(TAO)　is　a　crucial　step　in　the　manufacturing　process　of　the　portal　milling　machine　(PMM).　Traditional　design　approaches　often　consider　only　the　machining　errors　arising　from　geometric　errors.　However,　the　thermal　characteristics　of　the　bi-rotary　milling　head　(BRMH),　which　significantly　machine　tool　accuracy,　are　frequently　overlooked.　Hence,　a　novel　TAO　model　of　PMM　is　proposed,　considering　the　thermal　characteristics　of　BRMH　across　multiple　operating　conditions.　Firstly,　based　on　the　multi-body　system　(MBS)　theory　and　homogeneous　transform　matrix　(HTM),　a　mapping　function　relating　geometric　errors　to　tolerance　and　volume　errors　is　developed.　Secondly,　the　heat　generation　and　dissipation　mechanisms　of　the　BRMH　are　analyzed,　and　precise　boundary　conditions　for　thermal　simulations　are　determined.　Notably,　the　spin　friction　torque　of　the　rolling　body　on　the　bearing,　which　contributes　to　heat　generation,　must　be　considered.　Finally,　the　established　accuracy　design　optimization　model,　which　balances　total　cost　and　machining　accuracy,　is　solved　using　the　NSGA-II　algorithm.　The　Pareto　optimal　solution　set　reveals　an　11.74%　reduction　in　total　cost　and　improved　machining　accuracy　for　the　PMM.　Besides,　the　proposed　framework　for　accuracy　design　optimization　with　thermal　characteristics　is　applicable　to　the　manufacturing　processes　of　other　machine　tools.