The present invention discloses a construction method for heuristic metabolic co-expression network and the system thereof. Based on the max-dependent criteria, the present invention treats the characterized multivariate mutual information of a plurality of metabolites as mutual function value, and applies an optimization searching for the best feature subset, with a heuristics computational intelligence multimodal optimization algorithm. And by running the optimization process in a plurality of times, combining and studying the results in each time running, a co-expression network structure is built. Finally, a threshold for segmentations is calculated through probability models, and an exact and stable metabolic co-expression network is obtained.