The health score is the average of the same page scores you see on the Pages tab, minus a capped deduction for site-wide issues. That one sentence explains most of the questions people ask about it.
Each page starts at 100 and loses points for the problems we find on it: a missing title, a title that's too long, no meta description, a broken image, thin content, a slow response, a missing canonical, and so on. More serious problems cost more, and a page that returned an error or couldn't be fetched is capped near zero. We average those page scores, then subtract a single deduction — never more than 20 points — for site-wide issues like a missing sitemap, a missing security header or a robots.txt that blocks something important.
Two kinds of page stay out of the average: pages your robots.txt told us not to fetch, and pages your server rate-limited or timed out on. We never saw them, so they count neither for nor against you.
Three consequences worth understanding:
A big site with a small problem scores better than a small site with the same problem. If ten pages are missing meta descriptions, that's a disaster on a 20-page site and a rounding error on a 2,000-page one. The score reflects that, correctly.
Scores from crawls of different sizes aren't comparable. If one crawl covered 1,300 pages and the next covered 2,600, you're averaging different populations. Compare crawls of similar size, or compare the issue counts directly instead.
Fixing one page barely moves it. To move the score you need to fix a class of problem across many pages: every product page missing a description, every blog post with the same title pattern. That's what the issue list is sorted for.
90 and above reads as Excellent, 70 to 89 as Good, 50 to 69 as Needs Work, and below 50 as Critical — the same bands used for an individual page score. Below 50, start at the top of the issues list and don't worry about the number until you've cleared the errors.
If your site score looks lower than the page scores in front of you, the site-wide deduction and the excluded pages are almost always the answer — "Why your site score is lower than your page scores" works a full example through, number by number.