Many partial differential equations defined on a rectangular domain can be solved numerically by using a domain decomposition method. The most commonly used decompositions are the domain being decomposed in stripwise and rectangular way. Theories for non-overlapping domain decomposition(in which two adjacent subdomains share an interface) were often focused on the stripwise decomposition and claimed that extensions could be made to the rectangular decomposition without further discussions. In this paper we focus on the comparisons of the two ways of decompositions. We consider the unconditionally stable scheme, the MIP algorithm, for solving parabolic partial differential equations. The SOR iterative method is used in the MIP algorithm. Even though the theories are the same but the performances are different. We found out that the stripwise decomposition has better performance.