Baggage allowance on connecting international flights?

I will be flying from CCU to Sydney next week on a student visa. First leg of my flight is on Jet airways which allows 30kgs of baggage but the second leg (Thai Airways) allows 20kgs. Even though they are not part of any alliance, Jet airways can through check in my luggage to That according to their website. I want to know if i have to pay excess baggage if i carry over 20 kgs( Less than 30) as thai allows only 20.