How to combine these two mysql queries to preserve the speed of it?

IN ( SELECT ... ) is usually vary inefficient. Avoid it.

All the answers so far are working harder than they need to. It seems like the JOINs are unnecessary until after the UNION. See more Notes below.

SELECT  Ads.AdId    FROM  Ads,     JOIN (        ( SELECT  AdId            FROM  AdsGeometry            WHERE  ST_CONTAINS(GeomFromText('Polygon(( -4.9783515930176 36.627100703563,                      -5.0075340270996 36.61222072018, -4.9896812438965 36.57638676015,                      -4.965991973877 36.579419508882, -4.955005645752 36.617732160006,                      -4.9783515930176 36.627100703563 ))'),                              AdsGeometry.GeomPoint)              AND AdId > 1000000 )         UNION DISTINCT         ( SELECT  ads_AdId AS AdId            FROM  AdsHierarchy            WHERE  locations_LocationId = 148022797              AND  ads_AdId > 1000000 )          ) AS nt ON Ads.AdId = nt.AdId    ORDER BY  Ads.ModifiedDate ASC

Notes:

• Both AdsGeometry and AdsHierarchy have adId (by different names); there is no need to do the JOIN in the inner queries, except possibly to verify that it exists in Ads. Is that an issue? My query will take care of in the outer SELECT's JOIN, anyway.
• UNION DISTINCT is needed because the two SELECTs may fetch the same ids.
• Move the > 1000000 inside to cut down on the number of values gathered by the UNION.
• The UNION will always (in older versions of MySQL) or sometimes (in newer versions) create a temp table. You are stuck with that.
• IN ( SELECT ... ) usually optimizes terribly; avoid it.
• I added some parentheses; It is possible (but not necessary at the moment) to add ORDER BY, etc, to the UNION; the parens make it clear what it would belong to.
• The only reason for the outer query is to get ModifiedDate for ordering. You could speed things up by removing that requirement. (The UNION probably creates a tmp table; this ORDER BY probably creates another.)

Both your UNIONqueries does extra work by searching for the results already found by doing

SELECT Ads.AdId FROM Ads WHERE AdId IN ...
or
SELECT Ads.AdId FROM Ads, (SELECT Ads.AdId ...) AS nt WHERE Ads.AdId = nt.AdId

Also SELECT Ads.AdId FROM Ads, ... GROUP BY Ads will probably be more efficient, as well as easier to understand if written as SELECT DISTINCT Ads.AdID FROM Ads, ...

Thus, this should give a better query:

SELECT DISTINCT AdId FROM  (SELECT Ads.AdId FROM Ads   INNER JOIN AdsGeometry ON AdsGeometry.AdId = Ads.AdId    WHERE       ST_CONTAINS(GeomFromText('Polygon((          -4.9783515930176 36.627100703563,          -5.0075340270996 36.61222072018,          -4.9896812438965 36.57638676015,          -4.965991973877 36.579419508882,          -4.955005645752 36.617732160006,          -4.9783515930176 36.627100703563       ))'), AdsGeometry.GeomPoint)   UNION ALL  SELECT Ads.AdId FROM Ads  INNER JOIN AdsHierarchy ON Ads.AdId = AdsHierarchy.ads_AdId  WHERE AdsHierarchy.locations_LocationId = 148022797) AS sub WHERE AdId > 100000

Some databases have different performance for INNER JOIN and LEFT OUTER JOIN.Just try next request and if it is slow please add EXPLAIN before SELECT and provide results.

SELECT DISTINCT Ads.AdIdFROM AdsLEFT OUTER JOIN AdsGeometry ag ON ag.AdId = Ads.AdIdLEFT OUTER JOIN AdsHierarchy ah ON ah.ads_AdId = Ads.AdIdWHERE ah.locations_LocationId = 148022797  OR (ST_CONTAINS(GeomFromText('Polygon((         -4.9783515930176 36.627100703563,          -5.0075340270996 36.61222072018,          -4.9896812438965 36.57638676015,          -4.965991973877 36.579419508882,          -4.955005645752 36.617732160006,          -4.9783515930176 36.627100703563      ))'), ag.GeomPoint))