why loop inside recursive function not complete in javascript

You only received the first node because you declared your for loop without the keyword var

for(i=0;i<treeArr.length; i++) By the time the first nodes array was traversed, i was equal to 3

Here are my comments on the rest of your code

var tree = [];
tree[0] = ["Node1", "Node2", "Node3", "Node4"] 
tree[1] = ["Node5", "Node6"] 
tree[2] = ["Node7", "Node8", "Node9"] 

//recursive function that checks if a node 
function schTree(treeArr){

    //FIX A
    //find out if element is an array
    if(Array.isArray(treeArr)){

    //FIX B
    //You did not declare i with var, meaning each recursive call
    //carried the prior value of i with it.
    //so after iterating over the first node, i = 3
    //which is greater than the length of node 1 and 2
     for(var i=0;i<treeArr.length; i++){

            //FIX C
            //removed inner length check, not needed
            //schTree checks for array before getting to this
            //point
             schTree(treeArr[i]);
      }
    }
    else {
        //While you'd probably want to do a clause for
        //objects, we'll assume only arrays here.

        //FIX D
        //Do something with the non array element
        console.log(treeArr);
    }
  }
  schTree(tree);