The Guangdong-Hong Kong-Macao Applied Mathematics Center Shenzhen Subcenter (referred to as the Subcenter) was established in 2023. The director of the Subcenter is appointed by the dean of the college and is located at Shenzhen University. It is jointly established by the Guangdong-Hong Kong-Macao Applied Mathematics Center and Shenzhen University, among other institutions.

The Subcenter focuses on applied mathematics and mathematical applications in core areas such as big data and artificial intelligence, modeling and computation in intelligent wireless communication, modeling and computation in precision medicine, partial differential equations in fluid mechanics and engineering computation, and intelligent logistics. Following the principle of "based in Shenzhen, radiating the Bay Area, facing the whole country, and looking at the world," the Subcenter conducts research on mathematical problems related to the major needs of industrial innovation and enterprise development in Shenzhen, especially the common and key technical problems related to mathematical applications. It breaks down organizational boundaries and disciplinary barriers, aiming to create a basic science center that integrates talent development, scientific research, and industrial services, contributing to the economic and social development of Shenzhen. The Subcenter is located on the third, fourth, and fifth floors of Huixing Building.