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The gridding is an essential task for DNA microarray image analysis which will definitely affect the spot segmentation and intensity extraction. The accuracy and reliability of existing gridding methods depend on the artificial experience value owing to they can not dynamically determine the required processing parameters. In this paper, the gridding problem is turned into an optimizing problem by using the natural feature of the signal points (gene points) which are arranged more regularly in the gene chip image. A new automatically searching method is put forward which based on heuristic algorithm to find the optimal solution for the optimization problem. It requires no human intervention. The outcome has shown that it achieves the auto-positioning effects for gene chip and the algorithm is simple with higher precision, it is also robustness.