Can I immigrate to Canada if I have a degree from SMU Sikkim Manipal University?

Yes, you can migrate to Canada or any other country even if you have any degree from SMU. The sole criteria for this is not a degree and you must fulfill other eligibility as well.  

The Comprehensive Ranking System for Canadian immigration is not based on whether you have a regular degree or a distance degree, given that the university must be recognized.

SMU is duly recognized by UGC for ODL programs. You can easily apply to Canada. Go for the ECA process at ICAS as they evaluate the application process at SMU. The management authorities are very supportive and they will help you in getting the transcripts.