We study the B-->phiK(S) decay in a supersymmetric (SUSY) SO(10) grand unified theory (GUT). We calculate the mass spectrum of sparticles for a given set of parameters at the grand unified theory (GUT) scale. We complete the calculations of the Wilson coefficients of operators including the new operators which are induced by neutral Higgs boson (NHB) penguins at LO using the mass insertion approximation (MIA) with double insertions. It is shown that the recent experimental results on the time-dependent CP asymmetry S-phiK in B-->phiK(S), which is negative and cannot be explained in the standard model (SM), can be explained in the model where there are flavor nondiagonal right-handed down squark mass matrix elements of second and third generations whose size satisfies all relevant constraints from known experiments (tau-->mugamma, B-->X(S)gamma, B-s-->mu(+)mu(-), B-->X(s)mu(+)mu(-), B-->X(s)g, DeltaM(s), etc.). At the same time, the branching ratio for the decay can also be in agreement with experimental measurements.