In recent years, there has been an upsurge of researching and learning the Amoeba management model in China. Amoeba management model is a business model created by INAMORI KAZUO in KYOCERA, and then many enterprises have achieved unprecedented success. At present, a large number of scholars have studied the amoeba management model, but the exploration of the operation mechanism of the amoeba management model has not yet appeared. As for an organization management model, it is very important to explore the mechanism for its normal operation, which provides the research question for this article, namely, the operation mechanism of amoeba organization model. Therefore, based on the characteristics of Amoeba organization, this paper explores the operation mechanism of Amoeba’s organizational model, which provides reference for other enterprises that want to implement the Amoeba organization model. The research found that the operation mechanism of Amoeba’s organizational model mainly includes Amoeba’s team relationship, team incentive mechanism, team accounting mechanism and team evaluation mechanism. The Amoeba team broke the traditional relationship between the corporate sector and the traditional relationship resulting in low efficiency of the enterprise, while the amoeba organization leads the trading relationship into the enterprise Amoeba teams, the trading between teams, and self-financing of each team resulting in the active communication between teams and the actively cooperate. The Incentive mechanism is mainly for the amoeba team decentralization, the establishment of a strict responsibility and profit mechanism for each team, the division of power and responsibility, so that each team has its own power. The accounting mechanism and the accounting of Amoeba organization model mainly introduce the independent accounting mechanism; each team is responsible for its own profit and loss, independent accounting, and uses the unit time accounting system to calculate the team. The Evaluation mechanism rigorously assesses the amoeba team. In the light of the strategy at this stage of the company, we need to build a guiding evaluation system so that the team goals and corporate goals become same, and commonly achieve the enterprise strategies.