Woocommerce payment gateway: disable payment gateway by shipping method.

function.php

<?php
/**
 * Woocommerce disable payment gateway by shipping method.
 */
add_filter( 'woocommerce_available_payment_gateways', 'venus_payment_method_by_shipping' );
function venus_payment_method_by_shipping( $gateways ) {
	if( is_admin() ) { // do nothing in /wp-admin
		return $gateways;
	}
	if( is_wc_endpoint_url( 'order-pay' ) ) { // "Pay for order" page
		$order = wc_get_order( wc_get_order_id_by_order_key( $_GET[ 'key' ] ) );
		if( $order->has_shipping_method( 'flat_rate' ) ) {
			if( isset( $gateways[ 'razorpay' ] ) ) {
				unset( $gateways[ 'razorpay' ] ); // unset cash on delivery if exists
			}
			if( isset( $gateways[ 'simpl-pay-in-3-for-woocommerce' ] ) ) {
				unset( $gateways[ 'simpl-pay-in-3-for-woocommerce' ] ); // unset cash on delivery if exists
			}
		}
	} else { // Cart/Checkout page
		// get a shipping method selected by a customer
		$chosen_shipping_method = WC()->session->get( 'chosen_shipping_methods' )[0];
		
		// check the shipping method
		if ( 'flat_rate:9' === $chosen_shipping_method ) {
			if( isset( $gateways[ 'razorpay' ] ) ) {
				unset( $gateways[ 'razorpay' ] );
			}
			if( isset( $gateways[ 'simpl-pay-in-3-for-woocommerce' ] ) ) {
				unset( $gateways[ 'simpl-pay-in-3-for-woocommerce' ] ); // unset cash on delivery if exists
			}
		}
	}
	return $gateways;
}