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In this study we proposed a robust watermarking algorithm to improve the watermark hidden. The watermark information is separated with the Chinese Remainder Theorem at first and then use Planted Plane Cubic Tree enumeration encoding topology structure. At last the sub-watermarking is hashed to the entire program code by chaotic system to protect the entire program code. In the extracting procedure the user inputs secret key to restore the graph structure into a watermark information to prove his copyright. The experiments indicate its robustness and stealthiness is stronger and more practicable.