In view of the new medical security system，on the basis of analyzing the relevant problems and challenges faced by medical institutions，this paper puts forward the countermeasures for budget management and cost control in the financial management of medical institutions，including: medical institutions should set up a separate cost accounting and budgeting department; Medical institutions need to optimize the relationship between the original cost accounting and performance allocation，improve the basic work processes such as hospital cost accounting and budget control，and strengthen the systematic management of cost accounting and budget management.