i have to send an email to a user in salesforce using email template.this template contain merge field type of custom object.
Messaging.SingleEmailMessage mail = new Messaging.SingleEmailMessage();
mail.setTargetObjectId(user.get(0).id);
mail.setTargetObjectId(user.get(0).Id)
mail.setTemplateId(specifier.get(0).Template_id__c);
mail.saveAsActivity = false;
mail.setWhatId(custom_object.Id);
i read in documentation If you specify a contact for the targetObjectId field, you can specify a whatId as well. This helps to further ensure that merge fields in the template contain the correct data. The value must be one of the following types: Account Asset Campaign Case Contract Opportunity Order Product Solution Custom
but if we are sending email to a user not to contact then how to assign a custom object for merge field type in custom objects as in the above code
Not sure this is possible to do, but it depends on the relationship between your custom object and your users that will be receiving the merged emails. Do you have a 1-to-1 relationship between User and CustomObject? If so, perhaps adding a reference to the single custom object instance that each user object references and then adding custom formula fields on your user object with CustomObject__r.CustomField__c would do the trick.
In a custom formula field on your User object:
TEXT(CustomObject__r.CustomField__c)
Then your template could be changed into a User template and the merge fields would be the formula fields that actually pointed to your custom object instance. But if you have some other relationship like 1-to-many or many-to-many between User and CustomObject__c, I think you're out of luck.