Today I was upgrading Vcenter 5.5 to 6.01 and face the below error during pre upgrade check .

The system name in the vCenter Server 5.5 SSL certificate and the vCenter Single Sign-On 5.5 SSL certificates are not compatible. Please replace either the vCenter Server SSL certificates or the vCenter Single Sign-On SSL certificates so both vCenter Server and vCenter Single Sign-On SSL certificates use the same system name.

The resolution that I followed was as below

Re-installing the vCenter Server stack

1. Completely uninstall in this order:vCenter Server
   vCenter Inventory Service
   vSphere Web Client
   vCenter Single Sign-On
2. Rename the following directories underC:\ProgramData\VMware to ensure new certificates are generated using the correct hostname.
   1. CISto old
   2. Infrastructureto old
   3. SSLto old
   4. VMware VirtualCenterto VMware VirtualCenter.old
   5. vSphere Web Clientto vSphere Web Client.old
3. Re-install vCenter Single Sign-On, vSphere Web Client, vCenter Inventory Service, and vCenter Service, and  ensure to reconnect to existing database.
4. Reconnect all of the hosts to the vCenter Server.

• After completing, attempt to upgrade the vCenter Server 5.x to 6.0.