I have a city limit so I need to destroy some cities, at the same time I don't want to lose the territory 

Currently the only way is to ransack your city, then immediately build an outpost in that territory

thank you,did not even think about it

You can also "merge cities" after getting a specific tech in Medieval (military administration or something?), but the cost is always so damn high that I don't know if anybody's ever used it in a practical way.

The influence cost of merging cities is mostly the missing infrastructure between them. If you painstakingly go down the list and build up the infrastructure, the cost will go down quite a lot (had my first two cities merged late game just for fun of it and it was something like 40k)