add_action( 'woocommerce_thankyou', 'bdev_email_subject_and_message_based_on_payment_gatway', 10, 1 );
function bdev_email_subject_and_message_based_on_payment_gatway( $order_id ) {
    if ( ! $order_id ) return;

    // get the order details
    $order = wc_get_order( $order_id );

    // get the customer information by getting their name and email using billing_XX_name and billing_email
    $customer_complete_name_and_email = $order->billing_first_name . ' ' . $order->billing_last_name . ' <' . $order->billing_email . '>';

    // shop owner and/ or shop details
    $headers = 'From: Shop Name <name@example.com>' . "\r\n";

    // cod = cash on delivery
    if ( get_post_meta($order->id, '_payment_method', true) == 'cod' ) {
        $subject = 'your subject';
        $message = 'your custom message here';
    }

    // cheque = check payment
    elseif ( get_post_meta($order->id, '_payment_method', true) == 'cheque' ) {
        $subject = 'your subject';
        $message = 'your custom message here';
    }

    // your standard payment option
    else {
        $subject = 'your subject';
        $message = 'your custom message here';
    }
    if( $subject & $message) {
        wp_mail($customer_complete_name_and_email, $subject, $message, $headers );
    }
}


// BONUS
// This is how you can find out all your active payment gateways and their slug
// looking at line 15, cod is the slug of cash on delivery
// run this code once, write down your slugs and then remove it
// the slugs will be shown on the shop page
function bdev_your_active_payment_gateways() {
    if ( is_user_logged_in() ) {
    $current_user = wp_get_current_user();
    if (user_can( $current_user, 'administrator' )) {
    echo '<span style="font-size: 25px; color: white; display: block; background-color: red; text-align: center; border-radius: 30px;">These are the activated payment gateways on your website</span><br><br>';
    foreach(WC()->payment_gateways->get_available_payment_gateways() as $payment_gateway)
    echo '<div><b>Gateway Name:</b> '.$payment_gateway->title .' <br> <b>'.$payment_gateway->title .' Slug:</b> '.$payment_gateway->id .'<br><br></div>';
}
}
}
add_action( 'woocommerce_before_main_content', 'bdev_your_active_payment_gateways', 1 );