There are several reasons why Voldemort may have chosen Malfoy Manor as his base of operations, namely because it belonged to one of the wealthiest pure-blood families. He needed a place he could trust, which meant it had to be the home of a Death Eater, and Lucius Malfoy was not only one of the wealthiest but one of the closest. It was already covered in significant magical protection put in place by Lucius, which increased its appeal.