woocommerce_checkout_create_order_line_item.php

<?php
/**
 * Add custom meta to order
 */
function plugin_republic_checkout_create_order_line_item( $item, $cart_item_key, $values, $order ) {
  if( isset( $values['pr_field'] ) ) {
    $item->add_meta_data(
      __( 'Your name', 'plugin-republic' ),
      $values['pr_field'],
      true
    );
  }
}
add_action( 'woocommerce_checkout_create_order_line_item', 'plugin_republic_checkout_create_order_line_item', 10, 4 );

order item meta saves in wp_woocommerce_order_itemmeta table
and gets with $order->get_items(); method