By default, mu4e sorts messages by date, in descending order: the
most recent messages are shown at the top. In addition, be default
mu4e shows the message threads, i.e., the tree structure
representing a discussion thread; this also affects the sort order:
the top-level messages are sorted by the date of the newest
message in the thread.
The header field used for sorting is indicated by “V” or
“^”9, indicating the sort order
(descending or ascending, respectively).
You can change the sort order by clicking the corresponding column with the mouse, or with M-x mu4e-headers-change-sorting (O); note that not all fields can be used for sorting. You can toggle threading on/off through M-x mu4e-search-toggle-property or Pt. For both of these functions, unless you provide a prefix argument (C-u), the current search is updated immediately using the new parameters. You can toggle full-search (Searching) through M-x mu4e-search-toggle-property as well; or Pf.
Note that with threading enabled, the sorting is exclusively by date, regardless of the column clicked.
If you want to change the defaults for these settings, you can use the variables
mu4e-search-sort-field and mu4e-search-show-threads, as well as
mu4e-search-change-sorting to change the sorting of the current search
results.