To relieve the enrollment pressure on Anshun Junior High School and Wenxian Junior High School in Tainan City, the Tainan City Government's Education Bureau decided in 1995 to establish Tainan Municipal Heshun Junior High School adjacent to Heshun Elementary School. The planned school site was mostly privately owned land, and there were challenges in gaining local landowners' understanding during the acquisition process. Initially, Principal Shen Shuizhu of Tainan Municipal Anshun Junior High School concurrently served as the director of the Heshun Junior High School preparatory office. Later, the position was assumed by Lin Maosheng, former principal of Kaohsiung County's Tianliao Junior High School, who was transferred to Tainan City. The school campus covers an area of 3.91 hectares, situated in the "Wen Zhong 40" area between National Tainan Special Education School and Heshun Elementary School. Its primary feeder schools are Heshun Elementary School and Chang'an Elementary School. Heshun Junior High School is the 19th junior high school in Tainan City and was then the northernmost junior high school in the city.

At the outset of its planning, the Tainan City Government designated Heshun Junior High School as a model "learning-oriented" school, with a planned 60 classrooms. Construction of the school buildings commenced in three phases starting from 1999, with a total project cost of 640 million New Taiwan Dollars. The groundbreaking ceremony for the first phase, the main teaching building, took place on December 29, 1998. The architectural style of the school draws inspiration from traditional Minnan courtyard houses, emphasizing local cultural elements. The campus is designed with a park-like atmosphere, featuring an open concept without walls, and is structured in a manner reminiscent of ancient Chinese academies, with three sections divided into front and rear teaching areas.

In recent years, Heshun Junior High School has been deeply involved in technology education. In addition to establishing the Heshun Technology Center in 2019, the school also joined the Ministry of Education's AI education program for elementary and junior high schools in 2020, achieving outstanding results. For instance, it was recognized as an excellent school in both 2021 and 2022, with its team of teachers consistently winning national awards in AI lesson planning competitions.

Heshun Junior High School has emerged as a crucial hub for advancing technology education in Taiwan.