Indeed. It was to limit the number of representatives the slaveholding states would have in Congress. It was a compromise between the non slave states who wanted the slaves to not be counted at all and the slave states that wanted all the slaves counted so that they would bring more proslavery representatives to Congress and thus make things like limiting the exportation of slavery to the territories impossible or at least much harder to accomplish. The compromise kept the slave states from being overwhelmed ab initio in Congress while not permitting them to overwhelm the antislavery states. Anything else would have precluded the Union.
People forget that slavery was just one of many issues that were dealt with. The Civil War resulted from this stupid compromise because of the Northern states taking economic advantage of the Southern states due to their increased power in government. Slavery in the United States would have died out once improved mechanical processes came along to the extent that the cost/profit bottom lines called for it. This compromise, in essence, created a future war between the two factions as one side, the North, was given an advantage in power that they abused.