I opened up the woocommerce source file and found the reason of the problem.
This problem caused because woocommerce sending email to user based on email in the order billing information, not in the user information.
Following procedure will solve the problem.
1. Open up the plugin/woocommerce/classes/class-wc-order.php
2. Fine codes shown in the first line below and then replace them with second line.
//original
$this->send( $order->billing_email, $subject, $message, $headers, $attachments );
//replacement
$this->send( get_userdata($order->user_id)->user_email, $subject, $message, $headers, $attachments );