Key parameters describing the spatial variability of soil properties based on the random field theory are the scale of fluctuation (SOF) and coefficient of variation (COV). To characterize the spatial variability of soil properties, reducing the impact of these errors and uncertainties is necessary. To accomplish this, for the five main layers of soil, we collected 18 cone penetration test (CPT) data from a highly heterogeneous region in Lianyungang New Airport, Jiangsu Province, China, and used the control variable method to analyze the influence of the estimation method of tendency, its function type and outliers. The results show that, compared with the ordinary least square method (OLSM), the least absolute deviation method (LADM) can more truly reflect the trend component of CPT parameters in the vertical direction, and the influence of other factors on SOF and COV is also studied, such as outliers and estimation functions of trend components. On this basis, a reasonable calculation process of SOF and COV is summarized, which provides a reference for the calculation of SOF and COV in vertical direction in the future. By comparing the SOF calculated by different models, the results show that the squared exponential (SQX) model has the highest SOF in 68.3% of the evaluation, and the single exponential (SNX) model has the lowest SOF in 64.4% of the evaluation. Moreover, we compared the SOF and COV of cone tip resistance (qc) and sleeve friction (fs), which showed that SOF of qc and COV of qc is lower than that of fs in 54.4 and 73.3% of all evaluations, respectively.