We test the recent claim that supersymmetric matrix quantum mechanics with mass deformation preserving maximal supersymmetry can be used to study N=4 super Yang-Mills theory on RxS^3 in the planar limit. When the mass parameter is large, we can integrate out all the massive fluctuations around a particular classical solution, which corresponds to RxS^3. The resulting effective theory for the gauge field moduli at finite temperature is studied both analytically and numerically, and shown to reproduce the deconfinement phase transition in N=4 super Yang-Mills theory on RxS^3 at weak coupling. This transition was speculated to be a continuation of the conjectured phase transition at strong coupling, which corresponds to the Hawking-Page transition based on the gauge-gravity duality. By choosing a different classical solution of the same model, one can also reproduce results for gauge theories on other space-time such as RxS^3/Z_q and RxS^2. All these theories can be studied at strong coupling by the new simulation method, which was used successfully for supersymmetric matrix quantum mechanics without mass deformation.