How do they count the time? My flight from Mongolia to Harbin, transit in Beijing for 3 hours.

Actually, the time is counted in a very logical way. It starts to be counted from your first scheduled landing in mainland China and it stops to be counted at the time of your last scheduled departure from China. If the entire time from your first scheduled landing, until your last scheduled departure is equal or shorter than 24 hours, you are eligible for 24 hour visa free transit. If it is longer just for a minute, you need to obtain a Chinese visa obtained in advance. The best thing, if you want us to help you, is to present your itinerary clearly and with the times of scheduled arrivals/departures. Here in your text you have been mentioning three Chinese cities (Harbin, Beijing and Chengdu), so it is not possible for us to tell you anything decisive until we see your itinerary and the times associated with it.