I used string to concatenate new object to an existing object.
private static void concatJSON() throws IOException, InterruptedException {
JSONParser parser = new JSONParser();
Object obj = parser.parse(new FileReader(new File(Main.class.getResource("/file/user.json").toURI())));
JSONObject jsonObj = (JSONObject) obj; //usernameJsonObj
String [] values = {"0.9" , Date.from(Calendar.getInstance().toInstant()).toLocaleString()},
innermost = {"Accomplished", "LatestDate"},
inner = {"Lesson1", "Lesson2", "Lesson3", "Lesson4"};
String in = "Jayvee Villa";
JSONObject jo1 = new JSONObject();
for (int i = 0; i < innermost.length; i++)
jo1.put(innermost[i], values[i]);
JSONObject jo2 = new JSONObject();
for (int i = 0; i < inner.length; i++)
jo2.put(inner[i], jo1);
JSONObject jo3 = new JSONObject();
jo3.put(in, jo2);
String merger = jsonObj.toString().substring(0, jsonObj.toString().length()-1) + "," +jo3.toString().substring(1);
System.out.println(merger);
FileWriter pr = new FileWriter(file);
pr.write(merger);
pr.flush();
pr.close();
}