I have a 3S LiPo battery with a balancing port and a JST port. I wanna plug it into my FlySky TH9X which has a 3 pin connector. Any suggestions how can I manage to connect it?

You might have got the JST along with battery holder right. Just desolder or cut them and connect it to your battery.
If you don't have one you may need to purchase that connector which is available in few electronic stores.
If nothing works then open your 9x and solder wires across supply and put a connector of your choice and do the same thing to you battery.

Keep a check on polarity on the 9x, the center pin is positive and outer pins are negative on the TH9X. This radio has a reputation of frying when the polarity is reversed.