Abstract: Aiming to the puzzle of advancing security quality on secret-related personnel of national defense scientific research, the affecting factors of security quality are discussed. Data is acquired by investigating in the form of question paper, and quantitative model about security quality is constructed with structural equation mode. Five endogenous latent variable are “security consciousness”, “security attitude”, “security knowledge”, “security skill”, “psychological pressure”; and three exogenous latent variable are“atmosphere of research team”, “management of organization”, “macro-environment“. The results show that: “atmosphere of research team” is the factor which exerts higher frequency influence, and “security skill”, is the sensitive factor which accepts higher frequency influence.