I've just learned a throrem which states that : A metric space has the structure of a topological space in which the open sets are unions of balls .
But the theorem only told me there "exist" one topology with respect to the metric.When we refer to topology on a metric space $S$ , do we mean the topology generated by open ball ?
Yes, a metric space $(S, d)$ induces a topology $\mathcal{T}$ which is generated by the basis $$\mathcal{B} = \{B(x, r) \ | \ x \in S \ \text{ and } \ r > 0\}$$
When authors refer to the topology on this metric space $(S, d)$, they usually mean the topology $\mathcal{T}$ above, which you can think of as the topology generated by open balls.