It would tough to suggest you anything without knowing more information here. Where are the CSV files location, are they available as lookup table file (under etc/apps/YourApp/lookups) OR they are regular CSV files that you can copy to Splunk search head server (under $SPLUNK_HOME/var/run/splunk) OR they are indexed into Splunk under an index and sourcetype?? There will be different method/command to retrieve the data from both CSV based on this (inputlookup OR inputcsv OR regular base search). Once that is available, you can compare the data like this (again what all fields are there and what you want to compare will derive the result here), assuming there is a common field between those two CSVs...
[Search to get data from CSV1 | table commonfield fieldtocompare1 field2compare2... | eval from="CSV1" | append [Search to get data from CSV2 | table commonfield fieldtocompare1 field2compare2... | eval from="CSV2"] | chart limit=0 values(fieldtocompare1) as fieldtocompare1 values(fieldtocompare2) as fieldtocompare1 over commonfield by from
This should give you fields like fieldtocompare1:CSV1 and fieldtocompare1:CSV2 which you can compare using eval or something.
