Lack of nutrients in the soil affects soil fertility which can hinder the growth and yield of any crop. Therefore, soil amendment is important to improve soil nutrient either by organic or inorganic technique. In this paper, we considered different inorganic fertilizers to determine the main optimal effect and their interaction on the yield of crop by adoption of mixed-level factorial experiment. Three inorganic fertilizers namely Nitrogen (N), Phosphorous (P) and Potassium (K) were considered each at different levels using tomato crop for investigation. We set up a multiple linear model to match with the design. We estimated the model parameters with the error component and sums of squares. A 2×3×4 design structure for factorial combinations—of factor N at two levels, factor P at three levels, and factor K at four levels using a randomized complete block design with three replications—was developed. Normality of the data was tested and factors visualization for both main and interaction effects were illustrated by the use of graphs. The result revealed that Nitrogen (N) and Potassium (K) concentration are significant while Phosphorous (P) concentration is not, the effect of two-factor interactions for NP and PK are not significant and NK is significant, which signified that the yields do not depend on the levels irrespective of the factor. Based on the results, we concluded that phosphorus is the best inorganic fertilizer compared with Nitrogen and Potassium in terms of soil nutrient for the yield of crops.