In manufacturing systems, there are environments where the elaboration of a product requires a series of sequential operations, involving the configuration of machines by stages, intermediate buffer capacities, definition of assembly lines and routing of parts. The objective of this research is to develop a modeling and statistical analysis of complexity in manufacturing systems under flow shop and hybrid environments. The methodological approach starts with the structural modeling, then the measurement of the complexity in the systems is developed, the hypotheses are proposed and finally an experimental and factorial statistical analysis is developed. The results obtained corroborate the hypotheses proposed, where statistically the structural design factors and the variation of production time per stage have a significant influence on the response variable associated to the total complexity. Similarly, there is evidence of correlation between the performance indicators and the variable studied, in which the incidence with production costs stands out.