As the exploration of ultra-deep layers and the development of geothermal resources continue, obtaining more accurate downhole parameters becomes increasingly important. Flow measurement, in particular, is a complex parameter that presents significant challenges. In order to enhance the accuracy of the turbine flow logging tool, this research focuses on optimizing the turbine flow metering structure through a range of methods. A calculation model related to the measurement process is established, and the flow field characteristics in the flowmeter are analyzed using CFD software. The sensitivity of various geometric parameters to the meter coefficient is also analyzed, and the significance of 11 influencing factors is classified and optimized using the Plackett–Burman climbing test design. The Box–Behnken design method is then used to conduct an experimental design for the significant influencing factors, and the results show that the regression model fits the actual situation well. The response surface method is used to optimize the structural parameters, and an orthogonal experimental design is carried out for the selected non-significant influencing parameters to obtain the optimal structure combination. After optimization based on the response surface method, the stability of turbine flow measurement accuracy is improved by 34.5%.