The region is situated in the eastern part of Czech Republic, where its eastern part creates border with Slovakia. To the southwest it borders with South Moravian region, to the northwest with Olomouc region and to north with Moravian-Silesian region. The area of 3,964 sq. km makes the region third smallest in the Czech Republic.
The area has a very rugged nature. Majority of the landscape is hilly, mountain and upland type. Part of the region, in Morava drainage area, is a fertile flat land; Hana in Kromeriz Township and Slovacko in Uherske Hradiste Township.
The northern part of the region is enclosed by the mountain ranges, called Moravskoslezske Beskydy, Javorniky on the north with the highest peak Velky Javornik and Bile Karpaty towards south with the highest peak Velka Javorina. This mountain range also creates natural border with Slovakia. Southward of Moravskoslezske Beskydy are the highland areas called Hostynsko; Vsetinska and Vizovicka.
To the southwest of the region is the Chriby mountain range with the highest peak Brdo. Among Chriby and the earlier mentioned highlands stretches towards the west from Olomouc Township a ravine called Hornomoravsky uval, which runs through Kromeriz Township all the way to the Zlin Township. Along the river Morava, in Uherske Hradiste Township, stretches the ravine called Dolnomoravsky, which continues to the South Moravian region.
From west to the south, across both ravines, flows the biggest river in the region, Morava. Most of the rivers in the region flow to Morava.
Among the most important are the river Becva to the north and Otava to the south. Zlin region has a large amount of the protected landscape areas. The large areas consist of 2 protected landscape areas; Beskydy and Bile Karpaty, which together make approximately 30% of the protected landscape area (CHKO) Bile Karpaty and belong to the top 10 biosphere UNESCO preserves in the Czech Republic.
In the region, there are also many natural preserves and nature sanctuaries.