Water eutrophication is one of the most serious environmental problems in the world, and the concomitant bloom of blue-green algae has become a great threat to the aquatic ecosystem including inland lakes, leading to an array of economic, ecological and social problems. It has been characterized that some allelochemicals, i.e. fatty acids, derived from aquatic macrophytes can inhibit effectively the growth of blue-green algae. The relationship between the inhibitory effect of fatty acids on the growth of blue-green algae and the chemical structure of fatty acids can be summarized as follows: firstly, the more unsaturated bonds in fatty acid, the stronger on the blue-green algae growth inhibition; secondly, the shorter the carbon chain of fatty acid, the better on the inhibition of algal growth, and thirdly, fatty acids with odd-numbered carbon atoms are more effective than those with even-numbered ones on the growth of blue-green algae. In order to further reveal the time- and concentration-dependent growth-inhibiting scenario of fatty acids on blue-green algae, two mathematical models were constructed based on the experimental data obtained from the inhibitory effects of four 18-carbon fatty acids, i.e. α-linolenic acid (cis-9,12,15-octadecatrienoic acid), linoleic acid (cis-9,12-octadecadienoic acid), oleic acid (cis-9-octadecenoic acid), and stearic acid (octadecanoic acid) on the growth of toxic Microcystis aeruginosa. The first model was constructed based on the time-efficacy analysis of individual fatty acid on the growth of Microcystis aeruginosa. According to this model the half maximal effective concentration (EC ₅₀) and minimal inhibitory concentration (MIC) at varying exposure time can be calculated easily and quickly. The second model was constructed according to the time-efficacy analysis of multi-fatty acids (α-linolenic acids, linoleic acid and oleic acid complex) on toxic M. aeruginosa. These two kinds of models will lend fundamental support to the time- and concentration-dependent analysis of different fatty acids on the growth-inhibiting effects of algae. Compared to the experimental data, such models are practical, effective and accurate with respect to the time-efficacy relationship analysis of fatty acids on the growth-inhibiting of M. aeruginosa. These models are of important significance in two aspects. It will shed light on the design of most economical scheme for blue-green algae control and on the development of environmental friendly algaecide on the one hand, and on the other, it changes the macroscopic water bloom control into a micro-scale one and converts the conventional quantitative analysis to fine prediction and budget.