You've got some pronoun trouble. Five uses of 'they/their/them' is confusing. Which 'them' are you referring to?
Also, you use the word, "Before" to start your sentence. This is confusing because it can sound like you're saying "Before they did this they did this other thing."
This is better:
> Men once killed whales to meet survival and basic needs, but later they killed whales for money even though the whales were harmless.
Notice there's only one pronoun, prefaced clearly by the subject (men). Also notice that it is clearer to use "the whales" twice; if you put "they were harmless" it's unclear who "they" are because you have two subjects - men and whales.