Law number 22 year 1999 that is becoming the basic principle for city or regency to implement more autonomy in their governmental management needs to be followed up by the Organizational section by preparing and making policies of organizational management and carrying out position analysis in the City Government as well as formulating policies that facilitate any organizational management in the scope of City Government as it is directed by the valid laws. In carrying out these duty and function, the Organizational Section has to be able perform optimal works in giving services to the public as it is highly demanded in the era of local autonomy. This research was taken place in the Organizational Section of City Secretariat of Pekanbaru. Its ends are to analyze the performance of the Organizational Section and, at the same time, to identify the existing influencing factors by using the theory of performance approach. The research method used by the writer here is a descriptive research method where data are collected from documentations and indepth interviews. The writer has the Chair of the Organizational Section, his deputies, staffs at the office, the chief of the Employee Mutation Section of City Secretariat of Pekanbaru, and an employee of Badan Pengawas Kota (the City’s Watch) as the informants. From the analysis and interpretation made based on the found data, it can be concluded that the performance of the Organizational Section of City Secretariat of Pekanbaru in this era of autonomy is still low. This happens because of the lack of professionalism of the city’s employees and the inefficiency of the existing organizational structure. In order to improve the performance of the Organizational Section of City Secretariat of Pekanbaru, it is strongly suggested that this Section makes some real efforts and optimizes its works in accordance with duty and function – not just by making out abstract ideas or statements. To materialize this end, the employees must be more professional and capable. Here, what we need is more chances for those employees to get better education and training, as their works demands it. Beside that, we need more discipline employees. There should be about the responsibility of the authority for every employee in duty and function. The now existing structure needs to be improved by making good job description and distribution, clear command line from the boss to the employees, and well-coordinated relationship with the Employees’ Section, the City Watch, as well as the City Government.