A calorie is a calorie when you are speaking about it as a unit of energy, it is not true in the sense of nourishing the body. The chemical makeup and structure of the food you eat (fats, carbs, processed, whole, raw, cooked, etc) makes a big difference in how it is metabolized. For example, the Glycemic Index of the food in question will change how it behaves in the body.
Food is fuel, nothing more. Just like with other forms of fuel it's quality will determine how efficient it is at doing it's job. Eating 2,000 calories of whole foods every day will effect your health and body much differently then eating that same 2,000 calories but consuming processed garbage instead. When you eat is also important and often overlooked. Consuming 2,000 calories in three 666.66 calorie meals will not fuel the body as efficiently as eating 6 or 7 smaller meals throughout the day.
Food is only half of the health equation though, lifestyle comes into play as well. Getting exercise every day and making sure some is aerobic and some anaerobic, getting enough rest, drinking enough water, getting the right amount of sun, etc all play a part in your health that is as important as the quality of food you consume.