Introduction and hypothesis Transurethral catheterization in pressure-flow study (PFS) may interfere with the function of the lower urinary tract and produce an incorrect urodynamic diagnosis. We aimed to investigate the influence of a 7F catheter on urinary flow parameters in PFS and its significance for urodynamic diagnosis. Our hypothesis was that intubation causes adverse effects on urinary flow rate and further influences the urodynamic diagnosis. Methods We reviewed a urodynamic database of men and women referred for evaluation of lower urinary tract symptoms. The urinary flow parameters of PFS and free flow (FF) were compared. The influence of intubation on urodynamic diagnosis was determined by re-evaluating bladder outlet obstruction (BOO) and detrusor underactivity (DU), with the maximum flow rate of PFS (Qmax.P) being replaced by Qmax of FF (Qmax.F). Results We initially screened 1,791 patients and included 1,144 for the analysis. Overall, PFS had a lower Qmax (p < 0.001), longer flow time (p < 0.001), and a similar voided volume (p > 0.05). However, Qmax.P displayed inconsistent changing directions: Qmax.P decreased in 72.8% of male patients and 83.5% of female patients but increased in 14.7% of male patients and 9.5% female patients. Qmax.P was unchanged in the remaining patients. The urodynamic diagnosis of BOO and DU changed correspondingly in both the decreased group and the increased group when Qmax.P was replaced by Qmax.F. Conclusions Compared with Qmax.F, the changing directions and magnitude of Qmax.P varied with each individual, which could have a significant impact on urodynamic diagnosis. Thus, when a similar volume is voided in FF and PFS, and Qmax.P differs obviously from Qmax.F, replacing Qmax.P with Qmax.F for evaluating BOO and DU may be a sensible choice.