The origins of agriculture have been a focal point of interest in Southeast Asia because of the profound influence domestication of cereal crops had on the ancient inhabitants of the region. Historically, an emphasis has been placed on the movement of farmers from China into Southeast Asia during the Neolithic, however, the origin of agriculture in Myanmar remains unknown. Recently, stable carbon and oxygen isotope analyses have provided insight into the subsistence practices of two prehistoric communities, Oakaie 1 and Nyaung’gan, living in north-central Myanmar during the late Neolithic and early Bronze Age, ca. 1300 − 700 BCE, but lacked the temporal resolution to identify any changes in the intensification of agriculture. Here, we report new C and O stable isotope analysis of individuals from Oakaie 1, and the UNESCO World Heritage complex of Halin excavated between 2017 and 2020. With a longer chronological sequence —dating between ca. 2700 BCE and 1300 CE— Halin provides the opportunity to examine diachronic changes in these practices. The results suggest individuals from Myanmar had a mixed subsistence economy focused on C3/C4 resources during the late Neolithic to Bronze Age and a less variable subsistence focused on C3 resources in the Iron Age, possibly associated with the intensification of wet rice agriculture and changes in water management practices. Situated in north-central Myanmar on the edge of mainland Southeast Asia, we suggest that southwest China, with a subsistence economy of rice and millet, played a role in the movement of this mixed farming strategy into Myanmar.