Hi Ramesh,
As I understand, you want to create an association between two external content types in SharePoint 2010 and encounter the error.
You could adjust the BDC Model by hand. BDC model is an XML file and it contains sets of descriptions of one or more external content types, their related external systems, and information that is specific to the environment.
For more detailed information, you could refer to the article below.
The article below is about managing BDC models (SharePoint Server 2010).
https://technet.microsoft.com/en-us/library/Ee524073(v=office.14).aspx
And you also could set up a web service for the database to avoid the second Primary Key requirement.
The article below is about Creating BCS External Content Type Association in SPD - primary/foreign key limitation.
http://thebearhive.blogspot.com/2011/05/creating-bdc-external-content-type.html
The article below is about tooling Associations in SharePoint Designer 2010.
http://blogs.msdn.com/b/bcs/archive/2010/01/15/tooling-associations-in-sharepoint-designer-2010.aspx
There is a similar case:
https://social.msdn.microsoft.com/forums/sharepoint/en-US/8f55fd7c-de96-45cc-9644-3bed85e36fe8/error-when-creating-association-between-two-external-content-type
Best regards,
Sara Fan