The invention provides a better and suitable simplified representative unicellular whole-genome database creating method and application thereof. On one hand, the method can be effectively applied totrace samples or samples with smaller cell population to perform simplified genome database creation by optimizing primers and amplifying steps; on the other hand, by means of enzyme correction treatment, an enzyme treating step capable of specifically resecting uridine monophosphate can be applied to a simplified genome unicellular sample amplifying method, and amplification error rate can be remarkably reduced. Compared with the prior art, the method creatively applies an optimized and improved unicellular database creating scheme to simplified genome database creation of the trace samples or the samples with the smaller cell population; meanwhile, compared with the prior art, the method has the advantages of higher efficiency, simpleness, practicability, accuracy, small loss, low cost,good method repeatability, low error rate, great suitability for the simplified genome unicellular whole-genome amplification of the trace samples or the samples with the smaller cell population and ability in widening sample application ranges; meanwhile, the error rate is reduced, and detection accuracy is improved.