That's correct, you cannot retrieve this data via Graph API, nor any other API, afaik. Use the "standard" domain tools (or at least the ones that work with Azure AD DS).
Unable to retrieve Active Directory Organization Units with Microsoft Graph API
How can I retrieve the Active Directory organization units(OU) that have been synced to Azure using ADDS(Active Directory Domain Services)? According to: https://azure.microsoft.com/en-us/documentation/articles/active-directory-ds-admin-guide-create-ou/ User accounts, groups, service accounts and computer objects that you create under custom OUs will not be available in your Azure AD tenant. In other words, these objects will not show up using the Azure AD Graph API or in the Azure AD UI. These objects will only be available in your Azure AD Domain Services managed domain So, is this just a "not possible" using Graph Api? Or is there another way? Is it possible using a different Microsoft api other than Graph?