My flight is from Toronto to Istanbul through Vienna. Now I need to stay in Vienna and decided not the take the connecting flight. First, do they let me to cancel the connecting flight? Second,if I am not allowed to cancel it, can I just-while checking in- ask the agent at the airport to put Vienna as my final destination so I can collect it at Vienna, and tell them that I am not gonna take the connecting flight?(I am OK with paying any penalty for that... but would they let me do that?)
It is usually against airline rules but some people do so to get a lower fare. That is known as hidden city ticketing. For it to work, you should not check-in luggage and only do it for one-way or on the last leg, because any subsequent flights would get automatically cancelled by the airline.
What you need to do change the itinerary with the airlines. Most of them will be happy to do so for a fee plus the fare difference. The exact fees and amount depends on the rules of the fare you purchased. Assuming you have a return flight too, you would have to pay to change it as well, although if you do it once for both, the fees for changing will be charged once.