Some problems in modern atmospheric optics and its applications in optical engineering were discussed, and key points were given as follows: (1) Atmosphere could introduce severe troubles to advanced optical engineering systems; (2) It is necessary to consider optical properties of the atmosphere in the design of an optical engineering system; (3) It is necessary to use probability for describing the effect of atmosphere; (4) We could not estimate the effects of atmosphere on an optical engineering system directly from weather condition; (5) It is impossible to determine exactly an atmospheric parameter as a statistical average; (6) A single parameter C_n² is not enough to describe the optical property of atmospheric turbulence; (7) It is necessary to promote the accuracy of detection results of atmospheric parameters by optical instruments; (8) It is impossible to eliminate completely the effect of atmospheric turbulence on optical engineering systems; (9) It is not worth the effort to investigate some problems concerning ideal conditions for light sources and atmospheric conditions. Some valuable problems were proposed to investigate in the current stage of atmospheric optics.