Historic building renovation projects pursue multiple objectives, including heritage conservation, functional upgrading, and long-term operation. Their cost formation is characterized by incomplete information, high implementation uncertainty, and continuous intervention of operational requirements, making conventional construction-stage-centered cost control insufficient. Integrating value engineering with whole-process cost control, this study develops a three-stage framework of value identification, value balancing, and value coordination from the owner’s management perspective, and applies it to a single-case study of the Shanghai Guang’er Warehouse Renewal Project. The results show that front-loading surveys, functional analysis, and scheme comparison in the design stage can clarify investment boundaries; approval coordination, techno-economic comparison, and change-control closure in the construction stage can dynamically balance conservation requirements, functional needs, and cost inputs; and early leasing involvement, utility coordination, and tenant collaboration in the operation stage can reduce secondary renovation and transition costs. In the case project, the total cost was 17% lower than the design estimate, and the occupancy rate approached 100% within one year after completion filing. The study provides practical reference for whole-process cost control in historic building conservation and urban regeneration projects.