The dtutil command prompt utility is used to manage SQL Server Integration Services packages. You can use this utility to create folder destination SQL Server instance from commandline.
Syntax: Dtutil /sources ServeName /fc SQL;ParentFolder;NewFolderName
Create a folder on root node called Finance.
Dtutil /sources myserver /fc SQL;\;Finance
Now we create folder called as Payroll under Finance.
Dtutil /sources myserver /fc SQL;Finance;payroll
Connect to the SSIS instance using SSMS; you will see the folder created.