How to keep a filter on for only one of the dual axes and show percentage for bar chart?

Ideally when I add filter it impacts both the axis in dual chart. How to keep it for only one axis

There is no direct option to filter only one axis in the dual-axis graph. But we have alternatives available which can help you achieve this job.

To do that, let's create a calculated field like below-

Now drag the region to the column shelf and then number of records as well as created LOD to the rows shelf. Make LOD as dual-axis and format. Now use category in filter and this will be only applied to the LOD and not to number of records.