The height of the cloves at which they begin to flower, which is about 20 meters, is a factor that affects the clove harvesting procedure. This means that collecting cloves at height necessitates using tools that ensure worker safety. The agricultural industry is susceptible to ergonomic work risks resulting from several elements, such as worker characteristics, job demands and procedures, work organization, and environmental conditions. It is necessary to prioritize people as the critical consideration in defining work or human-centered design to manage ergonomic risks. This research analyzes the risk facts for clove flower pickers with a comprehensive method covering task, organization, and environment. This study was conducted during the clove flower harvest season from July to September 2023 at the plantation in Munduk Village-Bali, with 107 participants. Data on ergonomic hazards from internal and external factors before and after work were collected from MSDs and predicted using the Nordic Body Map questionnaire; fatigue was measured using the Core questionnaire Quality of Life (EORTC QLQ- C30), rating pulses were measured using a pulse meter. The data obtained were analyzed using SEM (Structural Equation Model). Significant differences were p < 0.05. The results of the research show that internal factors, particularly age, exert a negative influence on productivity. External factors, including body posture, time conditions, social conditions, information conditions, and human-tool interactions, significantly influenced productivity. This highlighted the importance of optimizing the "human-machine-environment" system to enhance safety, efficiency, and overall well-being.