Even if the pronoun wasn't there, this sentence would still translate to "It is my garden", since garden in English is an it. "He is my garden" would sound at least awkward.
And as you will notice (if you haven't already), there are many words in Greek which are either masculine or feminine, that are actually neuter in English.
I'm afraid that English native speakers (or really, any kind of speaker that'd learning a foreign language) sometimes have to be rational and take the rules of their own language into account as well. ^.^