If A registered in Karnataka and booked B, Maharashtra registered vehicle for carrying the goods to C- Hariyana, the freight is paid by A. In this case whether i need to pay IGST or CGST\ SGST under RCM.

Reply—Since A is making payment to Goods transport agency, liability of payment of tax under reverse charge is also on 'A'.  

Applicability of IGST or CGST and SGST depends upon Place of supply of service and location of supplier. As per section 7(3) of IGST Act, 2017, subject to the provisions of section 10, supply of services, where the location of the supplier and the Place of supply are in two different states  shall be treated as a supply of goods in the course of inter-State and IGST should be charged.

In case of GTA service, as per section 12(8) of IGST Act, 2017, the Place of supply of services by way of transportation of goods, including by mail or courier to,––
(a) a registered person, shall be the location of such person;
(b) a person other than a registered person, shall be the location at which such goods are handed over for their transportation.

In your case Place of supply u/s 12(8) is Haryana (location at which goods are handed over)

As per section 2(15) of IGST Act, 2017, the term location of the supplier of services means

(a) where a supply is made from a place of business for which the registration has been obtained, the location of such place of business;

(b) where a supply is made from a place other than the place of business for which registration has been obtained (a fixed establishment elsewhere), the location of such fixed establishment;

(c) where a supply is made from more than one establishment, whether the place of business or fixed establishment, the location of the establishment most directly concerned with the provision of the supply; and

(d) in absence of such places, the location of the usual place of residence of the supplier

If location of supplier is in different state and Place of supply is in different state, IGST should be charged. Therefore, as per your query:-

As transporter is registered in Maharashtra then location of supplier is in Maharashtra thus IGST will be paid under RCM.