The topology of quantum systems has become a topic of great interest since the discovery of topological insulators. However, as a hallmark of the topological insulators, the spin Chern number has not yet been experimentally detected. The challenge to directly measure this topological invariant lies in the fact that this spin Chern number is defined based on artificially constructed wave functions. Here we experimentally mimic the celebrated Bernevig-Hughes-Zhang model with cold atoms, and then measure the spin Chern number with the linear response theory. We observe that, although the Chern number for each spin component is ill defined, the spin Chern number measured by their difference is still well defined when both energy and spin gaps are nonvanished.