We discuss the supersymmetric CP problem that arises when the sfermion soft mass universality is modified. We place the 3rd generation SU(5) ten-plet sfermion masses in the weak scale in view of the naturalness. The other sfermion masses are assumed to be universal and a TeV scale in order to weaken the flavor changing neutral current processes and electric dipole moment (EDM) constraints. However this modification generically induces too large up quark chromo-EDM (CEDM) via the weak scale stop loop. In order to suppress this CEDM, we propose certain type of flavor structure where the parameters of the up-(s)quark sector are real whereas those of the down-(s)quark and the charged (s)lepton sectors are complex at the GUT scale. It is shown that, in this set up, up quark CEDM can be suppressed within the range where the current and future experiments have their sensitivity. We briefly illustrate the simple realization of these particular forms of the modified sfermion universality with real up-(s)quark sector by spontaneous CP violation in E\(_6\) SUSY GUT with SU(2) flavor symmetry.