Transit visa

Met, you have mentioned 3 hours, but it is obvious that your transit through China will take more time because you have mentioned that you will have two airports for your transit and here we talk about Chengdu (Tianfu) and Shanghai airports. So, if this is the case, you should just take care that your entire transit time in China, counted from your first arrival in China (it will be probably Chengdu) until your last departure from China (it will be probably Shanghai), is not longer than 24 hours.

So, if your entire transit time is not longer than 24 hours, you will be covered by 24 hour visa free transit and you do not need any kind of visa. Please, have in mind to use correct terminology because this is not a transit visa, but visa free transit, so there is no visa at all. You are advised to print out your flight tickets and have them at hand as copies ready to be shown to the Chinese authorities. One detail more. If Chengdu is your first stop in China, the first thing you will do upon landing is to approach transit counter where you will apply for a temporary enter permit by presenting your flight tickets. This permit is free of charge, but it is necessary because your flight from Chengdu to Shanghai will be a domestic one. Now I hope that this explanation is clear enough, but if it is not, you are free to ask for additional clarification.

Sorry, make me clarify:

From Turkey To Japan:
Istanbul - Shangai - Tokyo (3 hours transit time at Shangai airport)

From Japan to Turkey:
Tokyo - Chengdu - Istanbul ( 4,5 hours transit time at Chengdu airport)

Do I need to apply for transit visa or directly continue to my next flight already arranged via transit gates/hall?

Thanks

No, you don't need any visa, just transit directly for both ways.