Practice, context and domain-specific knowledge.

#1 is easy, #2 requires some investigation, #3 requires studying.

If you're looking at say, banking code - but you know nothing about finance - you may struggle to understand what it's doing. You may want to gain some domain expertise. Being an SME makes reading the related code a heck of a lot easier.

Context comes down to learning the code base. What code calls the part you're looking at? What user actions trigger it? Look at the comments and commit messages - what was the intention? This just takes time and a lot of trawling around, looking for patterns and common elements. User manuals and documentation can also help. This part can't be rushed - it just comes to passing over it again and again and again. If you have access to people very familiar with the code - ask them! They may be able to kick start your intro.

#1 will come naturally with time.

Very good advice!

To add to the above; IME, #3 comes first. Study the domain to understand the concepts and their relationships. Read some books/Articles, Watch some Videos, Read Documentation etc. to come up to speed on the terminology/jargon and the general concepts/ideas. Then, in order to understand their mapping to the specific application at hand, sit with the local "guru" (there is always at least one in every group) and pick his/her brain for a few sessions (getting them brown bag lunches works great for this) on the overall architecture of the System. Next sit with testing and use the app as an end-user to understand use-case scenarios which brings all of the above together.

During all the above stages, take copious notes, draw diagrams/graphs/etc. use source code analysis/documentation/browsing/etc. tools eg. doxygen/cscope/opengrok/etc. tools to navigate the codebase and cement understanding. Note also that the above stages are to be done both iteratively and parallelly until you are somewhat comfortable and not necessarily know/understand everything.

With the above in hand, pick one use-case scenario, preferably the most complicated, critical and important one and walk through the code from beginning to end for that path. Remember that you are trying to get the overall picture and hence treat all irrelevant details as blackbox abstractions during initial phases. Over time as you iterate and review the code again and again you can slowly add in the details for a more comprehensive understanding.

Finally, there is no shortcut to the above; it takes time and self-effort. We Humans are natural-born, trial-and-error, continuous-learning problem solvers and so trust to your intelligence and commonsense to find a path to move ahead when stuck at something.