You need to use one or more columns common to both as a key, something like:
SELECT T1.MyKeyCol, T1.MyDataCol
FROM
[Excel 8.0;HDR=YES;Database=C:\File1.xls;].[Sheet1$] AS T1
INNER JOIN
[Excel 8.0;HDR=YES;Database=C:\File2.xls;].[Sheet1$] AS T2
ON T1.MyKeyCol = T2.MyKeyCol
;
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