總結了兩種方法：

一、父級的複選框禁用

<el-tree
    :data="deptOptions"
    node-key="id"
    :props="defaultProps"
    :expand-on-click-node="true"
    :filter-node-method="filterNode"
    :check-strictly="true"
    show-checkbox
    ref="tree"
    @check="handleNodeClick"
/>

<script>
    export default
 
{
        data:{
            defaultProps:{
                children:'children',
                label:'name',
                disabled:function(data,node){
                        if(data.children&&data.children.length>0){
                            return true            
                        }
 
else{
                            return false            
                        }
                }    
            }
        },
        methods:{
            handleNodeClick(data,checked, node){
                if(checked){
                    this.$refs.tree.setCheckedNodes([data]);
                }
            },
        }
    }
 
</script>

二、隱藏父級的複選框，css大法好嘢，真的好嘢

<el-tree
  :data="deptOptions"
  node-key="id"
  :props="defaultProps"
  :expand-on-click-node="true"
  :filter-node-method="filterNode"
  :check-strictly="true"
  show-checkbox
  ref="tree"
  @check="handleNodeClick"
/>

<style lang="scss" scoped>
::v-deep .el-tree {
  // 不可全選樣式
  .el-tree-node {
    .is-leaf + .el-checkbox .el-checkbox__inner {
      display: inline-block;
    }
    .el-checkbox .el-checkbox__inner {
      display: none;
    }
  }
}
</style>