The microalgal research field is currently lacking a unified theoretical computing system to explain various experimental results related to microalgal growth. Thus a novel universal theoretical model was created to predict microalgal growth with carbon dioxide (CO2) fixation in any cultivation system. First, a new “light-effect colorimetric method” was proposed to estimate the actual f2 value of suspended microalgal cells during regular experimentation using a formula explaining the photosynthetic effective electron transfer rate (ETR = PFD·ΦII·f1·f2), which only requires the use of a simple spectrophotometer. A mathematical relationship between photosynthetic electron transfer and the microalgal growth rate was then identified based on this modified ETR by simplifying factors influencing the cultivation conditions (e.g., nutrients and CO2) into the slope and intercept of this formula. Subsequently, software was written to allow the above relationship to stimulate any 3-D microalgal cultivation system. Many example cases were conducted to clarify the significance and application of this theoretical model. It was found that the average ETR of a cultivation system describes microalgal tolerance to high CO2 concentrations. A photobioreactor at any given location under a certain light condition has a theoretical maximum yield of microalgal biomass, irrespective of how the other cultivation conditions change. A new concept of “biological similarity” is proposed as a basic principle for scaling up microalgal experiments with photosynthetic CO2 fixation to perform a repeated growth curve with < 5 % error. Finally, a “multi-batch dilution method” was demonstrated to increase the microalgal biomass yield by 64.4 % over a short cultivation period. General application of this calculation model would change the empirical status of microalgal engineering designs.