JSFiddle - React, Tailwind, and code Playground

JavaScript

var main_array = ["allen~1", "ajay~2", "raj~3"];
var sub_array=["allen", "ajay"];

var i, j;
for (i = 0; i < sub_array.length; i++) {
  for (j = 0; j < main_array.length; j++) {
    if (main_array[j].indexOf(sub_array[i]) != -1) {
      main_array.splice(j, 1);
    }
  }
}
        
alert(main_array);