Firstly of all, traditional Chinese medicine and Western medicine use different ways of organizing the information based on the same symptoms, same signs and same patient. Let me take an example. Diagnosing the same patient with a lump in her breast, a Western doctor will see a cyst, lesion, fibroid or cancer whereas a Chinese medical doctor will see a stagnation of Qi, Blood, or Phlegm. The Western doctor will seek to prove the diagnosis with a biopsy of the hardened tissue. The practitioner of Chinese medicine will feel the unique quality of the pulse at the radial artery which may feel "wiry" or kind of hard, like a guitar string bouncing up and down beneath your fingers (as opposed to other pulses that can feel softer and more flowing), observe the color and shape of the tongue looking for purple in particular, with possibly a thick yellow coating. Also used for diagnostic purposes will be seemingly unrelated symptoms such as a sensation of constriction in the chest, abdominal bloating, heightened emotional sensitivity and a tendency to be easily angered and frequent headaches at the top or the sides of the head. This will allow the doctor of Chinese medicine to sum up with a diagnosis of "Qi, Blood or Phlegm stagnation."
Secondly, what Western medicine tends to diagnose and treat is the effect that the disease state has on the body itself. The Practitioner of Oriental medicine diagnoses and acts upon the energy that creates the disease state. In other words, some believe that the greatest strength of Western medicine is in its trauma care and therapies for acute problems, while Chinese medicine excels in the areas of chronic problems and preventive medicine. Focus of Chinese medicine that the scientific world is still struggling to accept is an internal substance that the Chinese call "Qi". In the West it could be described as bio-electric energy. Acupuncture seeks to treat health on the level of Qi. There are pathways in the human body wherein this Qi flows. Western medicine can see and measure certain changes in the body's chemistry and functional activities with these conditions, but cannot act upon these changes for lack of understanding of their cause. The symptoms are too divergent and unrelated from a materialistic standpoint. But when you factor in Qi energy and its properties, all these conditions make perfect sense.
Thirdly, another aspect of the difference between Chinese and Western medicine can be described as Chinese treats the Yang and Western treats the Yin. Everything in the universe can be described in terms of Yin or Yang. This is one of the underlying philosophies of Traditional Chinese Medicine. When applied to medicine in general, Western medicine acts upon the Yin of the body, the substance of the body, the actual cells and chemicals. Traditional medicine works more on the energy that animates those cells.
Last but not the least, the concept of "side effects" is not recognized as such in Chinese medicine while in Western medicine bases on chemical materials and its side effects are sometimes stronger than the therapeutic roles. The toxic effects of certain Chinese medicines is recognized according to degree, and if it is necessary to use a 'toxic' substance medicinally, it will be prepared in a special manner or combined with other medicines to reduce or eliminate toxicity if possible. Traditional Chinese medicine is based on natural plants and its comprehensive and flexible treatment strategies always bring about fantastic treatment result. So more and more people in the world are interested in traditional Chinese medicine, and it is becoming a major medical stream in the world.