The "ify" part of both words is pronounced the same, the but the first part is pronounced differently: MOD-if-fye; MORT-if-fye.
Note: modify is very frequently used in US English, while mortify is rarely heard, and then only as a past participle in an expression like: "I'm mortified by this." I'm a native English speaker in the US, and I've never used "mortify" in speech or writing