Zirconium-based metal-organic frameworks (Zr-MOFs) possess excellent advantages of large surface area, high porosity, easy functionalization, simple and rich synthesis methods, and outstanding stability, which manifest great application potential in the fields of gas adsorption and separation, catalysis, and sensing. The appropriate level of defects can change physicochemical properties without destroying the structure of Zr-MOFs, significantly improving adsorption and catalysis performance. The structure of defects can be modulated using defect engineering, and the precise defect information can be obtained through a combined use of different characterization techniques, which accelerate the practical applications of defective Zr-MOFs in specific fields. Herein, defect modulation strategies such as template method and post-synthetic modification method, and defect characterization techniques of Zr-MOFs are discussed in detail, the advantages and disadvantages of different techniques are further discussed. Progress on defective Zr-MOFs in the field of chemical defense has been reviewed, including adsorption of toxic industrial chemicals, catalytic degradation of chemical warfare agents, gas sensing and separation, and their future developments are prospected.