The nucleon EDM is shown to be directly related to the EDM of atomic systems. From the observed EDM values of the atomic Hg system, the neutron EDM can be extracted, which gives a very stringent constraint on the supersymmetry parameters. It is also shown that the measurement of Nitrogen and Thallium atomic systems should provide important information on the flavor dependence of the quark EDM. We perform numerical analyses on the EDM of neutron, proton and electron in the minimal supersymmetric standard model with CP-violating phases. We demonstrate that the new limit on the neutron EDM extracted from atomic systems excludes a wide parameter region of supersymmetry breaking masses above 1 TeV, while the old limit excludes only a small mass region below 1 TeV.