Yep, you could use hitboxes. You can make image points in your enemy sprite and attach the hitboxes to these points. Use a every x seconds (like 0.2 or something, you don't need to refresh this every tick/60 times a second - 5 or 10 times a second is enough) condition to update position and scale of the hitboxes. If you enemy has several animation, you would have to set the points for every image in the animation and update the condition with the framerate of said animation.
Or you could do it like a boss and use a bone animator like spriter pro, which would allow you to build and animate your enemy in body parts. If you import this spriter animation with the construct plugin, you can click on each body part without additional hitboxes.