Hello,
I read the document about the rate-limits, will renew domain create a new order ?
The document says up to 300 new orders every three hours.
Welcome to the Let's Encrypt Community 
Yes. Acquiring a renewal certificate is generally no different than acquiring a new certificate.
This is a notable exception:
Renewals are treated specially: they don’t count against your Certificates per Registered Domain limit, but they are subject to a Duplicate Certificate limit of 5 per week.
A certificate is considered a renewal (or a duplicate) of an earlier certificate if it contains the exact same set of hostnames, ignoring capitalization and ordering of hostnames. For instance, if you requested a certificate for the names [
www.example.com,example.com], you could request four more certificates for [www.example.com,example.com] during the week. If you changed the set of hostnames by adding [blog.example.com], you would be able to request additional certificates.
Renewal handling ignores the public key and extensions requested. A certificate issuance can be considered a renewal even if you are using a new key.
Hi @levilu
please share your exact setup.
If you have some domains, you are not affected from that
rate limit.
That's only relevant if you have thousands of domains.