To　solve　the　potential　security　issue　caused　by　the　fact　that　the　transmitted　beam　in　the　phased　array-assisted　wireless　communication　systems　only　depend　on　angle　characteristics　and　high　computational　complexity　caused　by　the　traditional　iteration　algorithms.　A　secure　transmission　scheme　with　3D　secure　region　assisted　by　Random　Frequency　Diverse　Array　(RFDA)　and　Deep　Learning　(DL)　is　proposed　in　this　paper.　Firstly,　the　requirements　for　the　secure　communication　with　the　desired　user　within　3D　secure　zone　are　derived.　Based　on　it,　an　optimization　problem　is　formulated　to　maximize　the　lower　bound　of　the　secure　rate　of　the　considered　system.　Then,　an　optimization　scheme　based　on　deep　learning　is　proposed　to　design　the　beamforming　vector　and　Artificial　Noise　(AN)　vector,　so　as　to　reduce　the　computational　complexity.　Simulation　results　show　that　even　when　the　eavesdropper　is　located　at　the　edge　of　the　desired　user＇s　secure　region,　the　proposed　scheme　can　achieve　the　3D　secure　transmission,　and　ensure　the　received　confidential　information　in　secure　region.