The 5S system is a system of elimination, tidiness, cleanliness, continuous standardization and habitual behavior. Implementing the 5S system requires employee motivation so that the application of 5S becomes effective and sustainable. From year 2015 to year 2017, the performance of 5S system implementation at an automotive manufacturer had been fluctuate. In year 2020, the company has a mission to achieve Total Productive Maintenance Award which is prestigious in manufacturing industry. The results of the study show that there is a direct or positive influence between employee motivation towards the culture of 5S system implementation. This can explain that employee motivation has a positive effect on the 5S culture. The parameter estimation value of the highest employee motivation variable is on the Improve variable indicator which is considered to have a direct effect. The result indicates that the employee's needs for career development and information are met in the company. The highest value of cultural variable parameter estimation of 5S system implementation is on the Shine variable indicator which is considered to have a direct effect. The result indicates that most employees can apply cleaning practice and cleaning maintenance to goods and work areas compared to other 5S system steps.