The molecular inclusion powder of d-limonene in β-cyclodextrin was prepared by using a twin-screw kneader at a low water content. The influence of water and alcohol content on the formation of the inclusion complex was studied in comparison with the inclusion complex obtained by the micro-aqueous method. The inclusion fraction of d-limonene in the complex powder in β-cyclodextrin was much higher than that made by the micro-aqueous method. The marked differences in the inclusion fraction were observed particularly at the molar water ratio to β-cyclodextrin of less than 10. The inclusion fraction increased sharply with the increase in the kneading torque. This means that the energy of kneading increased the inclusion of d-limonene. A mathematical model for estimating the inclusion fraction was derived by combining the effects of water and the kneading energy on the formation of the inclusion complex.