As you know the episodes of Star Wars The Clone Wars were not aired in chronological order. So here’s the official chronological order of the series (with the 2 movies which are in between the show) :

Star Wars Episode II Attack of the Clones

216 Cat and Mouse
116 Hidden Enemy

T The Clone Wars theatrical release
3×01 Clone Cadets
3×03 Supply Lines
1×01 Ambush
1×02 Rising Malevolence
1×03 Shadow of Malevolence
1×04 Destroy Malevolence
1×05 Rookies
1×06 Downfall of a Droid
1×07 Duel of the Droids
1×08 Bombad Jedi
1×09 Cloak of Darkness
1×10 Lair of Grievous
1×11 Dooku Captured
1×12 The Gungan General
1×13 Jedi Crash
1×14 Defenders of Peace
1×15 Trespass
1×17 Blue Shadow Virus
1×18 Mystery of a Thousand Moons
1×19 Storm over Ryloth
1×20 Innocents of Ryloth
1×21 Liberty on Ryloth
2×01 Holocron Heist
2×02 Cargo of Doom
2×03 Children of the Force
2×17 Bounty Hunters
2×18 The Zillo Beast
2×19 The Zillo Beast Strikes Back
2×04 Senate Spy
2×05 Landing at Point Rain
2×06 Weapons Factory
2×07 Legacy of Terror
2×08 Brain Invaders
2×09 Grievous Intrigue
2×10 The Deserter
2×11 Lightsaber Lost
2×12 The Mandalore Plot
2×13 Voyage of Temptation
2×14 Duchess of Mandalore
2×20 Death Trap
2×21 R2 Come Home
2×22 Lethal Trackdown
3×05 Corruption
3×06 The Academy
3×07 Assassin
3×02 ARC Troopers
3×04 Sphere of Influence
3×08 Evil Plans
1×22 Hostage Crisis
3×09 Hunt for Ziro
3×10 Heroes on Both Side
3×11 Pursuit of Peace
2×15 Senate Murders
3×12 Nightsisters
3×13 Monster
3×14 Witches of the Mist
3×15 Overlords
3×16 Altar of Mortis
3×17 Ghosts of Mortis
3×18 The Citadel
3×19 Counter Attack
3×20 Citadel Rescue
3×21 Padawan Lost
3×22 Wookiee Hunt
4×01 Water War
4×02 Gungan Attack
4×03 Prisoners
4×04 Shadow Warrior
4×05 Mercy Mission
4×06 Nomad Droids
4×07 Darkness on Umbara
4×08 The General
4×09 Plan of Dissent
4×10 Carnage of Krell
4×11 Kidnapped
4×12 Slaves of the Republic
4×13 Escape from Kadavo
4×14 A Friend In Need
4×15 Deception
4×16 Friends and Enemies
4×17 The Box
4×18 Crisis on Naboo
4×19 Massacre
4×20 Bounty
4×21 Brothers
4×22 Revenge
5×02 A War on Two Fronts
5×03 Front Runners
5×04 The Soft War
5×05 Tipping Points
5×06 The Gathering
5×07 A Test of Strength
5×08 Bound for Rescue
5×09 A Necessary Bond
5×10 Secret Weapons
5×11 A Sunny Day in the Void
5×12 Missing in Action
5×13 Point of No Return
5×01 Revival
5×14 Eminence
5×15 Shades of Reason
5×16 The Lawless
5×17 Sabotage
5×18 The Jedi Who Knew Too Much
5×19 To Catch a Jedi
5×20 The Wrong Jedi
6×01 The Unknown
6×02 Conspiracy
6×03 Fugitive
6×04 Orders
6×05 An Old Friend
6×06 The Rise of Clovis
6×07 Crisis at the Heart
6×08 The Disappeared
6×09 The Disappeared: Pt. II
6×10 The Lost One
6×11 Voices
6×12 Destiny
6×13 Sacrifice

Darth Maul Son of Dathomir (2014 comics adapted from an unaired arc of season 6)
Story Reel: Death on Utapau
Story Reel: In Search of the Crystal
Story Reel: Crystal Crisis
Story Ree: The Bing Bang
Dark Disciple ( 2015 novel adapted from a season 7 arc)

Star Wars Episode III Revenge of The Sith