Scheduling in decentralized manufacturing systems is being expanded and transformed to a smart level where manufacturing tasks are executed autonomously. However, achieving self-organized manufacturing resources that can make collaborative decisions remains challenging. This paper presents a novel negotiation model for decentralized scheduling in an autonomous manufacturing system. A variety of emotions represent the willingness of autonomous intelligent agents (IAs) to negotiate for a consensus despite their diverse goals. The proposed communication protocol considers the emotional aspects of the autonomous machine agents in decentralized decision-making. The negotiation model focuses on analyzing the effects of two key emotions: selfishness and cooperation. This study constitutes the basis for experiments on multi-goal machine tasks and artificial emotion mechanism in a flow shop production system. The complexities of negotiation dynamics between IAs, where the interplay of selfish and cooperative strategies influences the outcomes and efficiency of reaching agreements, are explored. The experimental results show that selfish IAs eventually reach agreements through gradual compromise, but cooperative IAs, with their flexibility, can quickly achieve resolutions, especially when bargaining power is balanced. Aligning with the dual concern theory, this study reveals that while selfish IAs can dominate cooperative ones, the cooperative approach often leads to faster and more effective outcomes, regardless of the level of selfishness involved.