can we use connect a long pipe with space station and use vacuum for fuel transfer?

A pump can lift water about thirty feet. That's the height where the column of water in the pipe weighs the same as an equivalent column of air (and that's why deep wells use submersible pumps: they push the water up from below, instead of pulling from above and relying on atmospheric pressure to provide the lift). While fuel would be less dense than water, it's still much more dense than air, and the pressure of the atmosphere simply doesn't provide enough force to raise that column of fuel very far.