Health Score reflects the proportion of internal URLs crawled by Site Audit that don't have errors. It is a metric that has to be examined within context as it depends on:

To understand Health Score, it would be important to understand what issues are. 

Issues are a set of rules or filters which you can apply to all crawled pages for a complete audit of your site. Issues can be an error, warning or notice depending on the deemed level of importance. We term the more critical issues as "errors". These pre-set issues can be configured or new custom issues can be created.

Health Score = (1 - (<internal URLs with errors> / <total internal URLs>)) * 100

For example, Site A has 10 pages crawled while 2 out of these 10 pages have errors. Thus, Health Score = (1 - (2/10))*100 = 80%

On the other hand, Site B has 100 pages crawled but 80 of these 100 pages have errors. Thus, Health Score = (1 - 80/100)) *100 = 20%

This also means that while Site A has less pages crawled compared to Site B, due to the fact that the proportion of errors is lower for Site A, its Health Score is higher.

Note: By using the option "Turn off for this project" for "Errors", Health Score will be affected and for "Warnings" or "Notices", it will be not.