Tkinter: How to make Tkinter to refresh and delete last lines?

There are a few things here that need fixing. For one, you don't need to call update. Generally speaking you should never call it, though that rule can be broken once you understand why that rule exists. It's safe to call update_idletasks which is generally what you want if you feel the need to call update. Even that can be avoided with proper design.

Second, there is no need to delete the line and create a new line. The canvas widget has a method named coords which can be used to adjust the coordinates of an item.

Third, you can leverage the tagging feature of the canvas. Give each clock hand a tag with a suitable name (eg: "second", "minute", "hour") and you use that to tell the canvas which item to update.

Finally, get in the habit of either creating an application class, or putting your application code in a function. It makes it easier to solve the problem of not being able to call a function until it is defined, and makes it so that you don't have to use global variables.

Here is a working example:

import Tkinter as tk; import timefrom math import cos,sin,piimport sysclass MyApp(tk.Tk):    def __init__(self, *args, **kwargs):        tk.Tk.__init__(self, *args, **kwargs)        self.size=300        self.title("Clock")        self.w = tk.Canvas(self, width=320, height=320, bg="#456", relief= "sunken", border=10)        self.w.pack()        self.w.create_line(0,0,0,0, fill="#ffc", tags="hour")        self.w.create_line(0,0,0,0, fill="red", tags="minute")        self.w.create_line(0,0,0,0, fill="black", tags="second")        uzr1 = tk.Label(self, text="12", bg="#456" )        uzr1.place(x=160, y=13)        uzr2 = tk.Label(self, text="6", bg="#456" )        uzr2.place(x=160, y=303)        uzr3 = tk.Label(self, text="3", bg="#456" )        uzr3.place(x=310, y=160)        uzr4 = tk.Label(self, text="9", bg="#456" )        uzr4.place(x=11, y=160)        e = tk.Button(self,text="Quit", command=self.Quit)        e.pack()        self.update_clock()    def update_clock(self):        s=time.localtime()[5]        m=time.localtime()[4]        h=time.localtime()[3]        degrees = 6*s        angle = degrees*pi*2/360        ox = 165        oy = 165        x = ox + self.size*sin(angle)*0.45        y = oy - self.size*cos(angle)*0.45        self.w.coords("hour", (ox,oy,x,y))        degrees1 = 6*m        angle1 = degrees1*pi*2/360        ox1 = 165        oy1 = 165        x1 = ox1 + self.size*sin(angle1)*0.4        y1 = oy1 - self.size*cos(angle1)*0.4        self.w.coords("minute", (ox1,oy1,x1,y1))        degrees2 = 30*h        angle2 = degrees2*pi*2/360        ox2 = 165        oy2 = 165        x2 = ox2 + self.size*sin(angle2)*0.2        y2 = oy2 - self.size*cos(angle2)*0.2        self.w.coords("second",(ox2,oy2,x2,y2))        self.after(1000, self.update_clock)    def Quit(self):        self.after(700,self.destroy())app = MyApp()app.mainloop()