Objective To investigate Cronobacter spp. and Enterobacteriaceae contamination in nutritious noodles manufacture process and study the molecular typing and traceability analysis of Cronobacter spp. Methods Totally 101 samples were collected during the process of production, including raw materials, intermediate products, environment swabs, manufacturing facilities, personnel swabs and final products. Enterobacteriaceae and Cronobacter spp. were detected. And pulsed-field gel electrophoresis (PFGE) assay was utilized for the molecular typing of Cronobacter spp. Results The isolation rate of Enterobacteriaceae and Cronobacter spp. were 53.5% (54/101) and 29.7% (30/101), respectively. The detection rate of Enterobacteriaceae was the highest in the environment swabs(72.7%,16/22), and the prevalence of Cronobacter spp. was 50.0%(5/10)in the final products. A high degree of genetic diversity was observed among the 31 isolates with 20 pulse-types dispersed throughout the dendrogram. And the isolates could be grouped into 6 clusters. Conclusion It should be paid more attention that Cronobacter spp. contamination existed in nutritious noodles manufacturing process, which might be due to the contaminated materials. In addition, effective control strategies were supposed to be developed during the manufacturing process.