As soon as he touches the flowers, he will have unknowingly offered it to god.
I understood the above sentence like this :
As soon as he touches the flowers, he will provide the flower to god.
Is it right?
It can't be that, because the 'it' is singular. One could guess at a couple of possible singular antecedents for 'it' - the flower display, or the experience of touching the flowers. But, as Tdol suggests, it's not possible to answer without more context.