For study of engineering facts, generally the operation of batch plants was classified into two types. One is the operation of multi-product batch process which produce multiple products with the same processing paths, the other is that of multi-purpose batch process which produce multiple products through the different production routes (Reklaitis, (1990)). Also, according to Voudouris (1996), the multi-purpose batch plants are divided into two categories, sequential plants and non-sequential batch plants. In this paper we develop the completion times algorithm of nonsequential multi-purpose batch plants which have one unit in each stage under UIS policy. We also propose an efficient scheduling method for those plants. The proposed scheduling method composed two step approaches. In the first step, modified-RAES heuristics for initial solution of multi-purpose batch process scheduling was developed. At the second step, we suggested the Modified Simulated Annealing (MSA) method with adjusting parameters of Simulated Annealing (SA) by Ku and Karimi (1991). To evaluate the performance and efficiency of this study, we have tested about 200 problems and could get the outperformed results.