How to change my stop watch code into real time?

  using UnityEngine;
  using System.Collections;
   public class Counterstarted : MonoBehaviour
  {

     private int minutes, seconds,partofSeconds;

     // Use this for initialization
     void Start ()
     {

     }

     // Use this to increment the variables
     void CountDown ()
     {
             partofSeconds++;
             if(partofSeconds == 100) {
             seconds++;                                   // incrementing the seconds
                     partofSeconds = 0;
             }
             if (seconds == 60) {                         // checking if seconds value is 60, if true then incrementing the minutes and resetting the seconds to 0
                     minutes++;
                     seconds = 0;
             }

     }
     //
     void OnGUI ()
     {
             if(GUI.Button(new Rect(10,50,100,50),"start")) {
                     minutes = 0;
                     seconds = 0;
                     partofSeconds = 0;
                     InvokeRepeating ("CountDown", 0, 0.01f);
             }
             if(GUI.Button(new Rect(10,150,100,50),"cancel")) {

                     CancelInvoke ("CountDown");
             }

             GUI.Label (new Rect (10, 10, 150, 30), minutes.ToString ().PadLeft (2, '0') + " : " + seconds.ToString ().PadLeft (2, '0')+ " : " + partofSeconds.ToString ().PadLeft (2, '0'));

This is my code for stopwatch it is perfectly working for real time.

I've changed your code to use the internal time of the game which should be quite accurate:

 using UnityEngine;
 using System.Collections;
  
 public class Stopwatch : MonoBehaviour {
  
 public static float minutes;
 public static float seconds;
 public static float fraction;
 float startTime;
 public static bool startandstop;
 public GUIText referencetotext;
 public GameObject RefObject;
  
 public static float starttime = Time.time;
 void start() {
     fraction = 0;
      //referencetotext.text="TimerText";
     transform.position=RefObject.transform.position;
 }
 void Update() {
     if(startandstop){
         seconds = Mathf.Floor(Time.time - startTime)%60;
         fraction = Mathf.Floor(((Time.time - startTime)-Mathf.Floor(Time.time - startTime))*100);
         minutes = Mathf.Floor((Time.time - startTime)/60);
     }
     GameObject.Find("3D").GetComponent<TextMesh>().text = string.Format("{0:0}:{1:00}:{2:00}", minutes, seconds, fraction);
 }
  
 void OnMouseDown(){
     if(this.name == "start_butn"){   
         //drag.dragopt=false;
         startTime = Time.time;
         startandstop = true;
     }
     if(this.name ==  "sec_btn"){
         minutes = 0.0f;
         seconds = 0.0f;
         fraction = 0.0f;
         //Application.LoadLevel(0);
         startandstop = false;
         print ("printed");
         //drag.dragopt=false;
     }
     if(this.name == "stop_butn"){
         startandstop = false;
         //drag.dragopt=false;
     }
 }
 }

Hope that works for you,

Scribe