"From September 1854 I devoted my whole time to arranging my huge pile of notes, to observing, and to experimenting in relation to the transmutation of species." Charles Darwin, Autobiography
I don't think the scientific method, as we know it, was used at the time but Darwin was using the method (which, I strongly believe, it not the only way to do science). So Darwin was using observations to describe the pattern then making hypotheses to explain those pattern. Then Darwin made more observations and experiments to either refute or support those hypotheses.