You need to create a new jsonObj reference with every iteration of the loop:

for (int j = 0; j < X.size(); j++)
 {
  zBean aBean = (zBean)X.get(j);
  jsonObj = new JSONObject();
//^^^^^^^^^^^^^^^^^^^^^^^^^^^ add this line
  jsonObj.put(ID,newInteger(aBean.getId()));
  jsonObj.put(NAME,aBean.getName());
  jsonArray.add(jsonObj);
 }

Otherwise you are updating the same instance over and over again, and adding a reference to the same object many times to the array. Since they are all the same reference, a change to one of them affects all of them in the array.

Here is some code using java 6 to get you started:

JSONObject jo = new JSONObject();
jo.put("firstName", "John");
jo.put("lastName", "Doe");

JSONArray ja = new JSONArray();
ja.put(jo);

JSONObject mainObj = new JSONObject();
mainObj.put("employees", ja);

Edit: Since there has been a lot of confusion about put vs add here I will attempt to explain the difference. In java 6 org.json.JSONArray contains the put method and in java 7 javax.json contains the add method.

An example of this using the builder pattern in java 7 looks something like this:

JsonObject jo = Json.createObjectBuilder()
  .add("employees", Json.createArrayBuilder()
    .add(Json.createObjectBuilder()
      .add("firstName", "John")
      .add("lastName", "Doe")))
  .build();

JSONArray jsonArray = new JSONArray();

for (loop) {
    JSONObject jsonObj= new JSONObject();
    jsonObj.put("srcOfPhoto", srcOfPhoto);
    jsonObj.put("username", "name"+count);
    jsonObj.put("userid", "userid"+count);

    jsonArray.put(jsonObj.valueToString());
}

JSONObject parameters = new JSONObject();

parameters.put("action", "remove");

parameters.put("datatable", jsonArray );

parameters.put(Constant.MSG_TYPE , Constant.SUCCESS);

Why were you using an Hashmap if what you wanted was to put it into a JSONObject?

EDIT: As per http://www.json.org/javadoc/org/json/JSONArray.html

EDIT2: On the JSONObject method used, I'm following the code available at: https://github.com/stleary/JSON-java/blob/master/JSONObject.java#L2327 , that method is not deprecated.

We're storing a string representation of the JSONObject, not the JSONObject itself

I think it is a problem(aka. bug) with the API you are using. JSONArray implements Collection (the json.org implementation from which this API is derived does not have JSONArray implement Collection). And JSONObject has an overloaded put() method which takes a Collection and wraps it in a JSONArray (thus causing the problem). I think you need to force the other JSONObject.put() method to be used:

    jsonObject.put("aoColumnDefs",(Object)arr);

You should file a bug with the vendor, pretty sure their JSONObject.put(String,Collection) method is broken.

I found very good link for JSON: http://code.google.com/p/json-simple/wiki/EncodingExamples#Example_1-1_-_Encode_a_JSON_object

Here's code to add multiple JSONObjects to JSONArray.

JSONArray Obj = new JSONArray();
try {
    for(int i = 0; i < 3; i++) {
        // 1st object
        JSONObject list1 = new JSONObject();
        list1.put("val1",i+1);
        list1.put("val2",i+2);
        list1.put("val3",i+3);
        obj.put(list1);
    }

} catch (JSONException e1) {
    // TODO Auto-generated catch block
    e1.printStackTrace();
}             
Toast.makeText(MainActivity.this, ""+obj, Toast.LENGTH_LONG).show();

You can try this:

public static void main(String[] args) throws ParseException {

    String jsonString = "{\"a\": \"b\",\"features\": [{\"feature1\": \"value1\"}, {\"feature2\": \"value2\"}]}";
    JSONParser parser = new JSONParser();
    JSONObject jsonObj = (JSONObject) parser.parse(jsonString);

    JSONObject newJSON = new JSONObject();
    newJSON.put("feature3", "value3");

    appendToList(jsonObj, newJSON);

    System.out.println(jsonObj);
    }


private static void appendToList(JSONObject jsonObj, JSONObject toBeAppended) {

        JSONArray arr = (JSONArray) jsonObj.get("features");        
        arr.add(toBeAppended);
    }

This will fulfill your both requirements.