We report a measurement of the amplitude ratio r(S) of B-0 -> (DK)-K-0*(0) and B-0 -> (D) over bar K-0*(0) decays with a Dalitz analysis of D -> K-S(0)pi(+)pi(-) decays, for the first time using a model-independent method. We set an upper limit r(S) < 0.87 at the 68% confidence level, using the full data sample of 711 fb(-1) corresponding to 772 x 10(6) B<(B)over bar> pairs collected at the Upsilon(4S) resonance with the Belle detector at the KEKB e(+)e(-) collider. This result is obtained from observables x(-) = +0.4(-0.6-0.1)(+1.0+0.0) +/- 0.0, y(-) = -0.6(-1.0-0.0)(+0.8+0.1) +/- 0.1, x(+) = +0.1(-0.4-0.1)(+0.7+0.0) +/- 0.1, and y(+) = +0.3(-0.8-0.1)(+0.5+0.0) +/- 0.1, where x(+/-) = r(S) cos(delta(S) +/- phi(3)), y(+/-) = r(S) sin(delta(S) +/- phi(3)), and phi(3) (delta(S)) is the weak (strong) phase difference between B-0 -> D0K*(0) and B-0 -> (D) over bar K-0*(0).