Teams played each other twice on a home and away basis, before the league split into two groups after phase 1 matches were completed.
[1] On 21 August 2020, The Football Association of Wales received confirmation that the JD Cymru Premier has been granted elite athletic status by the Welsh Government, meaning that the 2020–21 season could commence on 11 September 2020.
[3] Flint Town United, runners-up of the Cymru North were promoted to the league due to champions Prestatyn Town's failure to secure a Tier 1 license.
[4] Similarly, Haverfordwest County, runners-up of the Cymru South, were also promoted due to champions Swansea University's failure to secure a Tier 1 license.
Teams that finished in positions fourth to seventh at the end of the regular season participated in play-offs to determine the third participant to enter the Europa Conference League first qualifying round.