Solution:
add_action('woocommerce_checkout_order_processed','custom_disount',10,1);
function custom_disount($order_id){
$order = wc_get_order($order_id);
$order_items = $order->get_items();
foreach ($order_items as $order_item_key => $order_item) {
$product = new WC_Product((int) $order_item['product_id']);
$quantity = (int) $order_item['qty'];
$discount=($product->regular_price*30)/100; //30% disount.
wc_update_order_item_meta($order_item_key,'_line_total',($product->regular_price*$quantity)-($discount*$quantity));
}
}