Arrayed　microlenses　have　been　demonstrated　as　promising　optical　devices　for　various　applications　in　optical　interconnection　and　communication.　The　precise　control　of　arrayed　microlenses　morphologies　still　keeps　a　main　challenge　restricting　its　practical　applications.　In　this　study,　we　propose　a　flexible　microlens　morphology　control　technique　based　on　the　pre-processed　femtosecond　laser　induced　periodic　surface　structures　(LIPSS)　morphology　control.　Anisotropic　elliptical　LIPSS　morphology　has　been　demonstrated　under　linearly　polarized　fs　laser　irradiation　due　to　the　grating-assisted　surface　plasmon　polaritons　scattering　effect.　Based　on　pre-processed　surface　structures　morphology　control,　polarization-dependent　geometrical　morphology　of　microlens　array　on　Si　can　be　obtained　with　controllable　morphologies　via　the　subsequent　isotropic　chemical　wet　etching.　By　varying　the　linear　polarization　direction　of　the　incident　fs　laser,　anisotropic　microlens　can　be　fabricated　with　the　major　axis　along　the　polarization　direction.　In　contrast,　symmetric　circular　morphology　can　be　obtained　by　controlling　the　morphology　of　the　pre-processed　surface　structure　to　nearly　circular　geometrical　morphology　under　circular　polarization.