The　problem　of　flexible　job　shop　batch　scheduling　represents　an　extension　of　the　flexible　manufacturing　problem.　Different　batching　strategy　significantly　affects　the　effect　of　subsequent　scheduling　optimization.　Therefore,　collaborative　optimization　of　the　batching　strategy　and　subsequent　scheduling　is　crucial　for　improving　production　efficiency.　In　this　paper,　a　flexible　job　shop　batch　production　model　considering　the　set-up　time　is　established　by　analyzing　the　coupling　relationship　between　batching　strategies　and　scheduling　optimization.　Based　on　the　proposed　model,　an　improved　genetic　algorithm　with　a　three-layer　coding　mechanism　is　developed　to　solve　the　problem　of　the　solution　space　expansion　caused　by　batch　collaboration.　The　three-layer　coding　mechanism　includes　the　batch　strategy,　operation　selection,　and　machine　selection.　In　addition,　an　operation　overlapping　strategy　is　introduced　to　improve　production　efficiency　and　make　production　more　resilient.　The　proposed　algorithm　is　tested　by　experiments　on　scheduling　problems　of　different　sizes.　The　experimental　result　shows　that　the　proposed　method　can　significantly　improve　and　efficiently　optimize　flexible　job　shop　scheduling　in　batch　production.