Objective: To analyze the health outcomes, cost and cost effectiveness of using testing methods to categorize patients with non-small cell lung cancer and guide targeted therapy. Method: Decision tree model was built to simulate that 3 groups of 100000 NSCLC patients respectively applied 3 ALK testing methods (FISH, Ventana IHC, and RT-PCR) recommended by China guideline and were treated with Crizotinib as first line if ALK positive. Medical cost occurred and health outcomes acquired in 5 years were calculated to carry out cost effectiveness analysis. Clinical and economic data were mainly retrieved from literature summary. Result: With 3 times of Shanghai GDP per capita (2014) as threshold (CNY292,110), Ventana IHC guided therapy group is less costly and more effective compared with PCR group; the ICER of FISH group versus Ventana IHC group was CNY1,091,727 /QALY, far more than the threshold, so Ventana IHC group was more cost effective than FISH group. Conclusion: Among 3 ALK testing methods, we suggested that Ventana IHC should be optimally selected as the companion diagnosis guided NSCLC targeted therapy in the disease management scheme.