Abstract: With the deficiency of the efficient of the Boolean SATisfiability (SAT) in the nano-meter CMOS circuit (CMOS/nanowire/MOLecular, CMOL) cell assignment resulted from the huge number of clauses and the big intermediate processing file, a novel approach using Pseudo-Boolean Satisfiability (PBS) to solve the CMOL cell assignment is proposed. The experimental results show that the proposed method can reduce the intermediate processing file efficiently by cutting down the number of the constraints without the additional Boolean variables introduced. The reduction of clauses and the intermediate processing file makes the proposed method work efficiently and improve the ability to deal with bigger circuits in contrast to the traditional SAT-based methods.