The governance system of the Edo period is known as the Bakuhan system, where the Shogunate (Bakufu) held authority over the Daimyo (Han), Hatamoto, and Gokenin. Directly controlled lands were called Bakuryo or Tenryo. Key locations were governed by officials such as Jodai, Shoshidai, Machi-bugyo, and Ongoku-bugyo, while other territories were managed by Gundai and Daikan.

Edo society was a feudal system dominated by the samurai class, centered around the Tokugawa Shoguns. The primary social structure was based on three main classes: the ruling samurai and the ruled peasants and townspeople. While samurai and farmers were previously not distinct, the fixing of residences clearly separated the classes (Shinonokōshō). However, there was some fluidity; famines often drove farmers into Edo, prompting the Shogunate to issue orders for them to return to farming. Additionally, there were Goshi (rural samurai) who lived independently. They were distinct from the Hanshi, who lived in castle towns and received stipends, and were often treated as a lower rank. Many figures active at the end of the Edo period came from these lower samurai or commoner backgrounds.

The relationship between the Shogunate and the Imperial Court is complex. The Shogunate strengthened its control over the Court through various laws and incidents. Scholars like Arai Hakuseki viewed the Shogunate's establishment as a revolution based on Neo-Confucianism, while others advocated for the delegation of authority. Conversely, some sought to restore Imperial power. Mito School scholars and thinkers like Yoshida Shoin argued for the legitimacy of Imperial rule, influencing the activists of the Meiji Restoration.

The Shogunate prioritized Machi-bugyo and Shoshidai in Edo, Osaka, and Kyoto, but also placed Daikan in strategic locations and mines. Their influence extended beyond cities, monitoring regional Daimyo and the Imperial Court. However, they possessed very little military force; the Nagasaki Bugyo in the early 18th century had only a dozen or so men, and the Gojo Daikan office at the end of the Edo period had only 30.