Can I use NC 3658.3 (Nuclear code) flange leakage methode for qualifing flanges in proces plant.(Where piping code is B 31.3) instead of ASME Sec VIII Div 1

If you apply ALL the specific requirements of ASME III to your process piping, then it might be appropriate use the simplistic approach in NC 3658.3. Otherwise it is very dangerous to cherry pick from such Codes.

I second MoverZ opinion: cherry picking equations and applying out of context is always dangerous.

In this particular case, that formula was first included in a work which was not in connection with Nuclear Code; it is Rodabaugh and Moore's "EVALUATION OF THE BOLTING AND FLANGES OF ANSI B16.5 FLANGED JOINTS".
The formula appears to be "dangerous" simple; in fact it is rather a simplistic "envelope" following complex stress flange calculations developed by authors. Later the formula was proposed by Mr. Rodabaugh for Nuclear Code.

For this reason, I think it is not "out of context" to consider the formula as a "reasonably good approximation of the moment limits calculated" for ANSI B16.5 flange.
Remains the reference problem; you would refer to that article not to ASME III!

In one one of the project I also used NC method for flange leakage as it was permitted in the design basis. I also have same doubt for applying NC method for process piping flanges. But still not clear.

NC method is based on bolt tension/stress. Flange and gasket parameters are not considered in calculation.

NC method appears to be based on bolt tension/stress but is something more complex. B16.5 Flanges and gasket parameters were considered in calculation, following a methodology that corrected the mathematical model Taylor-Forge and considered higher bolt stress (as in real life).
In the end of this work, the wizard- Everett C. Rodabaugh gave a simple formula that has been considered as a reasonable limit for all the stuff.

Today that formula seems to be simple and naive and nothing more.