Aiming at the prominent problems such as ambiguous identification of R&D activities

undifferentiated unified management

disconnection between business and financial data

and inconsistent statistical calibers existing in the R&D expense management of science and innovation enterprises

this paper constructs a six-dimensional two-tier evaluation index system integrating project control and financial control based on the FAHP-Tier grading algorithm. Four standardized calculation formulas are designed to realize quantitative scoring

and four Tier management levels (Tier0–Tier3) are divided according to comprehensive scores

matched with gradient 1S/2S/3S differentiated control rules covering special funds

special account books and independent R&D accounts. Corresponding hierarchical management specifications for project implementation

financial accounting and full-life-cycle intangible asset operation are formulated through multiple comparison tables. On this basis

a B/S integrated business-finance digital system with embedded FAHP computing module is developed

which supports multi-industry adaptive filling templates and automatic risk grading. Finally

the study summarizes the complete closed-loop logic from theoretical modeling to digital implementation

points out the limitations of single expert weighting and insufficient system data interface

and puts forward future optimization directions such as machine learning weight optimization and intelligent risk early warning. This research provides a quantitative standardized management paradigm and supporting digital tool for multi-industry and multi-scale innovative enterprises to standardize R&D expense compliance control.