Tds on csr contribution through ngo

Yes, You should Deduct TDS u/s 194C while remitting payment to NGO whether registered or not.

First tell me how TDS Applied on CSR Fund.

If the payment is for providing any CSR services to the company itself (or) to beneficiaries named by the company, then TDS will be attracted. 

If the discretion of choosing the CSR beneficiary or participant is with the company and not the CSR implementation partner or NGO, TDS should be deducted under 194J. 

For common donations or contributions made under CSR, TDS will not be attracted.