Ferromagnetism in topological insulators (TIs) opens a topologically non-trivial exchange band gap, providing an exciting platform to manipulate the topological order through an external magnetic field. Here, we experimentally show that the surface of an antiferromagnetic thin film can independently control the topological order of the top and the bottom surface states of a TI thin film through proximity couplings. During the magnetization reversal in a field scan, two intermediate spin configurations stem from unsynchronized magnetic switchings of the top and the bottom AFM/TI interfaces. These magnetic configurations are shown to result in new topological phases with non-zero Chern numbers for each surface, introducing two counter-propagating chiral edge modes inside the exchange gap. This change in the number of transport channels, as the result of the topological transitions, induces antisymmetric magneto-resistance spikes during the magnetization reversal. With the high Neel ordering temperature provided by the antiferromagnetic layers, the signature of the induced topological transition persists in transport measurements up to a temperature of around 90 K, a factor of three over the Curie temperature in a typical magnetically doped TI thin film.