The working behavior of face slab of concrete face rockfill dam (CFRD) is affected by the formation and development of cracks in underwater face slabs in operation period. In the purpose of revealing the causes of underwater cracks, the influences of unfavorable temperature conditions and construction quality on cracks of concrete face slab in operation period were analyzed based on monitoring data. A method was put forward to characterize the construction quality by the probability distribution function of void fraction. The construction defect area in rockfill area was simulated using quality assurance rate, and finally the process of analyzing cracks of concrete face slab in operation period was determined. With a CFRD as an example, the stress situation and change trend of the cracking area of concrete face slab were studied via structural calculation. Results suggested little influence of temperature factor on the generation and development of deep underwater cracks. When the quality assurance rate of rockfill construction in the construction quality defect area reached 90% under the action of water load, the calculated crack stress conformed with the crack inspection results, which verified the rationality of the simulation method. The research finding is of engineering significance for the safe operation of CFRD, and could be taken as reference for the cause analysis and judgment of underwater cracks of CFRD during operation.