The present invention relates to a method for improving an organism through the profiling of flux sum of metabolites, and more particularly to a method for screening key metabolites, the method comprises: plotting a profile between objective functions based on useful substance formation rate as a main function through an algorithm perturbing other functions influencing the production of useful substance; determining the utilization (flux sum (Φ)) of all metabolites from the profile; and screening key metabolites, which show an increase in flux sum (Φ) with an increase in useful substance formation rate. The present invention also relates to a method for improving an organism producing a useful substance, the method comprises introducing and/or amplifying genes associated with the screened key metabolites or introducing the genes from the outside into the organism. According to the disclosed invention, the metabolic utilization (flux sum; Φ) of specific metabolites according to an increase in useful substance formation rate can be predicted, so that key metabolites in increasing the production of a useful substance can be screened. Also, it is possible to increase the production of a useful substance through the method of improving a target organism by introducing and/or amplifying genes associated with the screened metabolites or through the method of supplying the metabolites during the culture of the organism.