Read google custom search limited to 100 results for more information.

Google Custom Search (GCS) has a limit of 100 search results for each query. These results are presented ten per page, for a total of ten pages. If you do not find your answer in these results, refine your query and search again.

If a search query produces fewer than ten pages of results, GCS search returns will still show navigation links for ten pages. Links to all pages beyond the last actual page will redirect to the final results page; for example, if a search produces only eight pages of results, then links to pages 9 and 10 will redirect to page custom search limited to 100 results

There’s a difference between two limitations:
a) max 100 queries per day
b) max 100 results per searched phrase (even split into 10 queries of 10 results per query).
The limitation (a) can be solved by paying to Google, whereas limitation (b) cannot be solved at all, it seems to be a feature of the CSE product when searching the whole web (i.e. not just a site search, which can give more results).

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