Background Deep brain stimulation (DBS) in the subthalamic nucleus (STN) is used in advanced Parkinson's disease (PD) for reducing motor fluctuations and the side effects of antiparkinsonian medication (APM). The development of neuroimaging has enabled the direct targeting of the STN. The aim of this study is to evaluate the outcome in patients with PD using STN DBS when changing from atlas-based indirect targeting method (iTM) to direct MRI-based targeting (dTM) assuming dTM is superior. Methods Twenty-five consecutive PD patients underwent dTM STN DBS surgery from 2014 to 2017 with follow-up for 1 year. The neuroimaging, surgical method, outcome in Unified Parkinson's Disease Rating Scale (UPDRS) scores, and reduction of APM are described and compared with the results of an earlier iTM STN DBS study. Results Twelve months after a dTM STN DBS, significant improvement (p < 0.001) was seen in six out of seven parameters of UPDRS when patients had medication (medON) and stimulation (stimON). The activities of daily living (UPDRSII) and motor scores (UPDRSIII) improved by 41% and 62%, respectively. Dyskinesias and fluctuations were both reduced by 81%. In dTM STN DBS group, the levodopa equivalent dose (LED) and the total daily levodopa equivalent dose (LEDD) were significantly decreased by 62% and 55%, respectively, compared with the baseline (p < 0.001). Five patients (20%) were without levodopa medication 12 months after the operation. Conclusions The development of surgical technique based on advanced neuroimaging has improved the outcome of PD STN DBS.