Metabolic conditioning is simply an elevated cardiovascular stress plus moderate to heavy strength efforts. That is, metabolic conditioning, or metcon, blends strength and cardiovascular efforts in a short, intense, and compact bout of exercise.
To get a bit more into the science of it, the term metabolic conditioning actually refers to the training of the various metabolic systems in the human body that store and deliver energy, of which the three are as follows:
The phosphagen energy system (high power/short duration): The phosphagen energy system fuels the most explosive and short-lived bouts of exercise, such as the first couple seconds of a sprint, a standing broad jump, or the swinging of a baseball bat.
The glycolytic energy system (moderate power/moderate duration): The glycolytic system kicks in after the phosphagen system is spent and fuels moderately intense bouts of movement, such as most strength-training and weightlifting efforts.
The oxidative energy system (low power/long duration): The oxidative energy system is the aerobic energy system; aerobic means with oxygen; the other two systems are anaerobic, meaning without oxygen. The oxidative energy system fuels lower-intensity and prolonged bouts of exercise, such as walking and distance running.
All three systems supply your body's molecular energy currency, adenosine triphosphate, or ATP; they just supply it at different rates. The phosphagen system, for example, supplies ATP quickly, but can only do so for a brief amount of time, whereas the oxidative system takes a little longer, but can supply ATP almost indefinitely. All your physical functions ultimately run on ATP.
The chief aim of metabolic conditioning is to increase the efficiency at which these systems store and deliver energy in the form of ATP — in simple words, to increase sheer work capacity — or the ability to do more physical work (both strength and cardiovascular) in the same amount or for longer periods of time.