There were two or three (depending on how you count them) main issues that caused this divide.
First (and second) there was the issue of slavery and slavery in the territories. The North had no slavery and the South did. In addition, there were disputes over whether slavery should be allowed in new territories such as those taken by the US from Mexico in the 1840s.
Third, there was the issue of nullification and secession (and states’ rights in general). This issue had arisen in the late 1820s with regard to tariffs. The South argued that states had the right to nullify federal laws and even to secede from the Union. The North did not agree.
These were the main issues that began the process of dividing the two sections.