How to parse array of array values in retrofit model class?

First of all correct your response format like this

{ 
"ModuleEId": [
    [
      "Test_SFPCA",
      "SFPCA_0001",
      "SFPCA_0002"
    ],
    [
      "Android_SFPCA",
      "SFPCA_0003",
      ""
    ]
  ]
}

You can parse using below code

try {

    JSONObject object = new JSONObject(response);
    JSONArray jsonArray = object.getJSONArray("ModuleEId");

    ArrayList<ArrayList<String>> mainArray = new ArrayList();
    for (int i = 0; i < jsonArray.length(); i++) {
        ArrayList<String> array = new ArrayList<>();
        JSONArray subJsonArray = jsonArray.getJSONArray(i);
        for (int j = 0; j < subJsonArray.length(); j++) {
            array.add(subJsonArray.getString(j));
        }
        mainArray.add(array);
    }

} catch (JSONException e) {
    e.printStackTrace();
}

OR

You can also create Model class

public class Demo{

    @SerializedName("ModuleEId")
    @Expose
    private ArrayList<ArrayList<String>> moduleEId;

    public ArrayList<ArrayList<String>> getModuleEId() {
        return moduleEId;
    }

    public void setModuleEId(ArrayList<ArrayList<String>> moduleEId) {
        this.moduleEId = moduleEId;
    }

}

Here is the valid json for your invalid json:

{
    "ModuleEId": [
        [
            "Test_SFPCA",
            "SFPCA_0001",
            "SFPCA_0002"
        ],
        [
            "Android_SFPCA",
            "SFPCA_0003",
            ""
        ]
    ]
}

Now you can parse it using this pojo class:

import java.util.List;
import com.google.gson.annotations.Expose;
import com.google.gson.annotations.SerializedName;

public class CheckResponse {

   @SerializedName("ModuleEId")
   @Expose
   private List<List<String>> moduleEId = null;

   public List<List<String>> getModuleEId() {
      return moduleEId;
   }

   public void setModuleEId(List<List<String>> moduleEId) {
      this.moduleEId = moduleEId;
   }

}

The simple and easiest way to parse your json response is to use

http://www.jsonschema2pojo.org/

copy your response and paste it on jsonschema2pojo and select your class name. It will return you java pojo code. You can easily utilize that to parse it.

Important: But your json response should be valid.

Hope this will help you.