This study analyzes with the technology of auto tuning using relay feedback test for non-square MIMO system through process modeling, identification, input-output pairing and control strategies. However, the control configuration selection based on conventional steady-state Relative Gain Array (RGA) matrix sometimes degrades the loop performance and it needs attention. This study also deals with the real challenges in time domain modeling and appropriate pairing of loops for non-linear chemical processes. The choice of input-output pairing for square system has been extended to non-linear chemical processes. This ensures the system’s stability by selecting an appropriate manipulated-controlled variable pairing in non-linear chemical processes and the same is also tested for benchmark of non-linear chemical processes. In this study, two types of non-square systems are considered: one is systems with excess input than output variables and the other is systems with excess output than input variables. Some benchmark non-linear chemical processes, such as processes with mild nonlinearity, moderate to high nonlinearity and highly nonlinearity, are also taken for this study. Three standard benchmark processes are used in analysis of nonlinear chemical processes, namely: (1) Continuous Stirred Tank Reactor (CSTR) process; (2) hydrogen-ion- concentration (pH) process and (3) distillation column and this procedure is illustrated via simulation of 3-by-2 and 2-by-3 non-linear chemical processes.