The invention discloses a codonNX system for optimizing woody plant genetic codons and an optimization method thereof. The system comprises an input module, a processing module and an output module, wherein the input module is used for inputting gene sequences and codon using frequency sorting tables by users and selecting specific processing modes; the processing module is used for receiving input codon information contents and codon using frequency sorting table information contents, carrying out effective processing according to the processing modes selected by the users, and outputting corresponding results through the output module. The codonNX system provides a complete developable total system gene optimization function so as to improve the working efficiency and save the cost; andparameters of the system are selectable, particularly, optimal codons are selectable, and all the parameters are open, transparent and selectable and can be set by users. The system is suitable for plant expression vector platforms, is relatively strong in pertinence, and is capable of obtaining high-expression proteins in transgenic plants via experimental verification.