In order to develop a methodology of analysis, mathematical modelling (simulation) and calculation of non-steady states in continuous mixing flow apparatus (CMFA), well-known dynamic differential equations are considered extended and solved for practical problems. Two types of non-steady states have been studied (1) the filling process in CMFA before continuous cultivation; (2) transient responses for continuous flow cultivation in CMFA prompted changes in process conditions (dilution rate and feed concentration). The theoretical analysis of these process dynamics shows the possibility of analytical solutions and satisfactory numerical calculation. Such methodology enables us to design the required filling process, to provide the optimal steady state for continuous cultivation and achieve the maximum biomass productivity for non-steady stares. The methodology is illustrated by experimental data and numerical examples for ethanol production from starchy raw material.