Determining habitat suitability is one of the most important elements of management and conservation of plant and wildlife species. A suitable habitat will have a significant impact on the survival and reproduction of species. Nowadays, the development of statistics and geographic information system has enables us to determine possible habitats for plant species via using geographical distribution modeling techniques. Using the Ecological Factor Analysis Model (ENFA), the present study has modeled the habitat of Fritillaria imperialis L., as a species with numerous industrial and pharmaceutical applications. To this end, species’ presence data was gathered with systematic sampling method with 500 presence points. Then the data was registered and then, the data was ultimately converted to a map of the vector format. Environment variable maps such as topographic, climate, and soil were generated by using geostatistical and GIS methods. Finally, the habitat map for this valuable species was generated. According to ENFA analysis, the variables of the amount of absorbable potassium, the amount of absorbable phosphorus, Digital Elevation Model, the amount of annual precipitation, and the slope direction of region, are the most significant factors, influencing the habitat selection for Fritillaria imperialis L in the study area. The amounts associated with being margininety, specialization, and tolerance in this study were 1.547, 6.325, and 0.158, respectively indicate that Fritillaria imperialis L is specialization species within its habitat sites. Boyes index was used to verify the correctness of this model, which was calculated to be 0.092. The results of the present study suggest that using alternative habitats can prevent the irreversible negative consequences like reduction or extinction of this valuable species.