The invention provides a method for separating and preparing hydrogen by decomposing water in a fuel cell through photocatalysis according to the inverse principle of the hydrogen fuel cell, aiming to avoiding the current separation problem of hydrogen and oxygen prepared by decomposing water through solar energy photocatalysis. The method adopts the inverse principle of the hydrogen fuel cell and uses photocatalyst as raw material for a photoanode, and platinum, nickel or carbon electrode as a cathode; an ion film is used between the two electrodes to transfer protons or hydroxyl ions, circuit is formed by connecting the photoanode and the cathode with a lead; sunlight or simulated sunlight is used as a light source, the light directly shines down upon the photoanode; and hydrogen is generated on the cathode and an oxidation reaction is performed on the anode so as to realize the aim of separating and preparing hydrogen by decomposing water through photocatalysis. In the method of the invention, no sacrifice agent or inhibitor is needed to add for adjusting the pH value of the electrolyte solution, an external power source can be added as additional bias so as to directly separate and prepare hydrogen by decomposing water through photocatalysis, and the separation problem of hydrogen and oxygen in practical technology development for decomposing water through solar energy photocatalysis is successfully solved.