In this work, we have investigated phase separation behavior in PS/PVP polymer blend thin films on gold substrates that have chemical stripes of different periods made by microcontact printing. The influences of pattern period and film thickness have been studied. The experiments have testified that the best result of phase separation, as shown in OM image, was obtained when the period of the chemical pattern is similar to the polymer particle size. Meanwhile, the film thickness plays a significant role on the phase separation. The best pattern replication in the polymer thin films only occurs in a relative narrow thickness range, for example, in this case between 30 and 60 nm. The possible interaction mechanism of the thin polymer film with the underlayed chemical pattern has been discussed.