Every amateur team in Indonesia competed in its provincial stage of the league and the teams which relegated from 2017 Liga 2 competed in the national zone preliminary round.
[2] Persik defeated PSCS 3–2 on aggregate to win their first Liga 3 title.
The following teams qualified from regional route for the national round.
There should be 40 teams relegated from 2017 Liga 2 competed in this route,[32][33] but Pro Duta and Persifa Fak-fak disqualified.
On 5 June 2018, PSSI disqualified PPSM Magelang and Sragen United.
[35] Later on 28 July 2018, PSSI disqualified Yahukimo because they didn't attend match coordination meeting in Gawalise Stadium.
Persijap hosted this group at Gelora Bumi Kartini Stadium.
[43] Perseka withdrew from the competition due to technical constraints.
PSBK hosted this group at Gelora Supriyadi Stadium, Blitar.
[37] PSGC hosted this group at Galuh Stadium, Ciamis Regency.