It　is　a　typical　irreversible　process　of　flow　and　heat　transfer　in　the　microchannel　and　it　is　necessary　to　reduce　the　irreversibility　to　improve　effective　utilization　of　energy　in　the　heat　transfer　process.　The　entropy　generation　rate　and　transport　efficiency　of　thermal　energy　are　derived　from　the　first　and　second　law　of　thermodynamics,　which　indicate　that　the　effective　utilization　of　thermal　energy　increases　with　the　decrease　of　net　temperature　gradient　of　fluid　in　the　micro　heat　sink.　A　new　micro　heat　sink　with　complex　structure　is　proposed　and　simulated　based　on　the　previous　study.　The　effect　of　structure　on　entropy　generation　rate　and　transport　efficiency　of　thermal　energy　is　also　analyzed.　The　results　reflect　that　the　less　the　net　temperature　gradient　of　fluid,　the　less　irreversibility　and　the　more　uniform　the　temperature　of　bottom　in　the　heat　sink.　Based　on　the　definitions　of　thermal　enhancement　factor,　entropy　generation　rate　and　transport　efficiency　of　thermal　energy,　it　is　reasonable　to　use　thermal　enhancement　factor　to　evaluate　the　comprehensive　performance　of　micro　heat　sinks,　while　the　other　two　are　used　to　measure　the　irreversibility　and　level　of　utilization　in　the　heat　transfer　process.　In　short,　the　evaluation　criteria　is　provided　by　the　first　law　of　thermodynamics,　while　the　essence　of　heat　transfer　enhancement　is　indicated　by　the　second　law　of　thermodynamics,　giving　a　complete　thermodynamic　theory　for　optimizing　micro　heat　sinks.　©　All　Rights　Reserved