I'm not sure what you mean, could you post an example, as a reprex?
The standard approach for merging dataframes is to use merge(), or left_join() from the package {dplyr}. The size of the dataframes and the way they were generated doesn't matter for this kind of merge by a key.
If you want to put the dataframes on top of each other (rbind() or bind_rows()) or side-by-side (cbind()orbind_cols()`) then the size is important, and you have to describe your expected result.