How to pass JavaScript array to Apex controller

You can use ActionFunction for this. Here is sample for your reference.

Controller:

public class ActionFunctionCLS {
  public Account actObj{get;set;}
   PageReference prf= null;
    public ActionFunctionCLS(){
      actObj = new Account();
    }

    public pagereference Saverec(){
   if(actobj.Name !=''){
    insert actobj;     
   }
   else{
     ApexPages.Message myMsg = new ApexPages.Message(ApexPages.Severity.ERROR,'Error: Please Enter Name.');
     ApexPages.addMessage(myMsg);      
   }
   if(actobj.id !=null){      
      // Send the user to the detail page for the new account.
      prf = new PageReference('/'+actobj.id);
      prf.setRedirect(true);       
   }
   return prf;
    }
}

VF Page:

    <apex:page controller="ActionFunctionCLS" id="pg" >
  <script>
   function recSave(){
    var accountType = document.getElementById('pg:fm:pb:pbs:actType').value;
    alert('accountType -->'+accountType);
    if(accountType != 'Prospect'){
     alert('You Should Select Prospect to Save the Record');
     return false;
    }
    else{
     saveAccount(); //this is the function name which calls our action function from java Script.
     return true;
    }
   }     
  </script> 

 <apex:form id="fm">
  <apex:actionfunction name="saveAccount" action="{!Saverec}" />
   <apex:pageBlock id="pb">
     <apex:pagemessages ></apex:pagemessages>
     <apex:pageblockButtons >
      <apex:commandButton value="Save" onclick="recSave();return false;"/>    
     </apex:pageblockButtons>       
     <apex:pageblockSection id="pbs">
       <apex:inputField value="{!actobj.Name}" id="actName"/>
       <apex:inputField value="{!actobj.type}" id="actType"/>
     </apex:pageblockSection>
   </apex:pageBlock>
 </apex:form>
</apex:page>

Note that we are calling Saverec Action from JS using saveAccount Action Function.