Geometrically　virtual　models　of　a　three-dimensional　polymerase　chain　reaction(PCR)　reaction　chamber　was　constructed　to　calculate　the　heat　flux　of　the　reaction　chamber　and　sample　using　Solid　Works　software.　The　temperature　distribution　of　the　reaction　system　was　performed　using　finite　element　software　ANSYS11.0　according　to　computation　thermal　method.　Numerical　simulation　results　showed　that　there　are　different　temperature　distribution　in　the　reaction　chamber　and　the　sample,　and　there　is　temperature　uniformity　in　the　chamber　bottom.　This　provides　theoretical　foundation　to　develop　a　self-design　real　time　PCR　instrument.