Matsuji is a reference to temples under the control of Honzan (head temple), but it had a different purpose when Honmatsu seido (the system of head and branch temples) was established, compared to the present day.
Before the Honmatsu seido was implemented, it was common to follow the sect and the system of teachings of the promoter (the one who had such a wish for a long time), who was the monk that founded or reconstructed the temple; however, there were cases when a powerful temple would suppress the neighboring middle and small temples and became "matsuji." Additionally, there was shinbutsu shugo (syncretism of Shinto and Buddhism) performed before the Meiji period, and even Shinto shrines were treated as matsuji. In extreme cases, the temples of different sects were forcibly made into matsuji.
As a result, the relationship between the head temple and matsuji was complicated; there were various relationships that focused on the head temple's finances by making it matsuji in order to contribute a part of its income from shoen (a manor in medieval Japan) and offerings (particularly, it sought donations for temples of different sects and shrines as a matsuji, as insurance to keep its original school and sect), or as a completely systemized relationship.
The Honmatu dispute (dispute over head and branch temples) rose from matsuji seeking its own independence from the head temple by having a great physical distance from the head temple, conflict due to different interests, or by having different sects, and the head-temple side sought to confirm the position and benefits of matsuji. The most famous one was Enryaku-ji Temple, which collected vast amounts of income from control over Gionsha, Shoren-in Temple in Kyoto City and surrounding areas and sought to further strengthen the base of its power, as derived from finance. Enryaku-ji Temple occasionally caused Honmatsu disputes; it stressed that Ninnan-ji Temple was matsuji during the Kamakura period ('Gamansho' (a book that advocates orthodox of To-ji Temple's Esoteric Buddhism and counters the misleading view of the followers of Mt. Hiei)) and suppressed Kitano-tenmangu Shrine during Bunan no Koji Sodo (Riot caused by rice malt sellers in the Bunan era) in Muromachi period and Hongan-ji Temple during the Kansei adversity (religious persecution during the Kansei era) to make them accept the matsuji of Enryaku-ji. Moreover, in the Sengoku Period (Period of Warring States), it burned down 21 head temples of the Nichiren Sect in Kyoto when they rejected its demand to become its matsuji through the excuse of sect conflict between the followers of the Nichiren Sect and Buddhist monks of Saito (Western Section) of Mt. Hiei (Tenbun Hokke War). Nevertheless, at the end of the Heian period Kofuku-ji Temple handed a appeal to the Imperial Court to recognize Enryaku-ji Temple as the matsuji. Other than that, controversies raised involving the Imperial Court and the bakufu (Japanese feudal government headed by a shogun), even beyond schools and sects, such as the one claiming by Todai-ji Temple to recognize To-ji Temple and Daigo-ji Temple as its matsuji.
Edo Bakufu established Honmatsu seido and tried to nullify the Honmatsu relationship between different sects in order to prevent massive political and religious conflicts.