"How come" and "Why" are the same?

How come you didn't call me last night?=Why didn't you call me last night?
Maybe there is slight difference.

I think you need to elucidate a little.
I'm unsure of what you're trying to ask!

I mean can I use "how come" instead "why"?

Are there any moderators at Antimoon? Just Tom and MJD now?

It's perfectly acceptable to use "how come" instead of "why" in British English but the former will tend to sound more colloquial.

Same for American English.

How come = Why is that? = emphatic
Why? = simple

Incidentally, it seems to be the same in Afrikaans, where one can say 'Hoekom'.

They are completely interchangeable, in my opinion. "Why" is the preferred usage, but you hear "how come" more frequently, at least in the parts of the US I've lived.