Sephiroth has a strange bond with his so-called "mother". He doesn't even know her before he burns down Nibelheim an kills a bunch of people, he even takes her from the Shin-Ra Headquarters five years later.
He sees her as his true mother although his real mother is Lucrecia and Jenova cells were just injected into her baby (Sephiroth). Although he does have a point; without the Jenova cells, he wouldn't be what he is today.
It is a bit strange that Sephiroth sees her as his true mother as she is supposedly an alien. But then again this is a madman we are dealing with and he couldn't really be seeing right, even if he is the great Sephiroth.