As the development of world-class eco-islands progresses, the homestay sector on Chongming Island has burgeoned, emerging as a pivotal catalyst for rural tourism and economic prosperity. This study, leveraging Chongming Island as a case study, systematically analyzes the spatiotemporal distribution of homestays across island-wide, township, and village scales, employing methodologies such as the spatiotemporal evolutionary tree model. It delves into the intricate systemic framework underpinning homestay development, elucidating the dynamics of interaction mechanisms. Furthermore, it examines the evolving roles of diverse stakeholders throughout various developmental phases, grounded in stakeholder theory. The study reveals that (1) Chongming’s homestays on the island, townships, and village scales show very obvious agglomeration characteristics, mainly concentrated in the A-level scenic spots and in and out of the island traffic junction. (2) The growth of homestays in Chongming shows an increasing trend year by year, with the growth rate slowing down after 2020, and can be divided into four main phases, which are closely related to the construction phase of the eco-island. (3) The evolution of Chongming Island’s homestay is a multifaceted natural–human system intricately shaped by a confluence of five interdependent subsystems: natural ecology, social culture, multiple stakeholders, geographical location, and transport infrastructure. At different stages of development, under the synergistic effect of multiple stakeholders, the homestays on Chongming Island eventually formed a governance structure led by the government and co-managed by the development company, external entrepreneurs, and local villagers. These insights not only augment the scholarly discourse on stakeholder dynamics within the homestay industry but also offer pragmatic enlightenment for strategic planning and the advancement of holistic urban–rural integration in Chongming and the broader Shanghai region.