With the continuous deepening of the reform of the scientific research funding system,the issue of cost control in scientific research institutions has also become increasingly prominent.In 2022,the Ministry of Finance formulated the"Specific Guidelines for Cost Accounting of Public Institutions-Scientific Public Institutions",providing guidance for cost accounting of scientific research institutions in public institutions.However,due to the late start of cost accounting in public welfare second class scientific research institutions,there are various issues of non-standard cost management,This article proposes suggestions and countermeasures for these issues,in order to effectively control the cost of promoting public welfare research units in the second category.