In this study we proposed self-assessment with prompts, learning journal and referencing through sharing learning methods for regulation of cognition with one annotation system called VPen. We also aimed to investigate the effectiveness of the learning methods on web-based programming learning performance and achievement. The results of this study revealed students perceived the learning methods are useful for the strategies of regulation of cognition. We also found that self-assessment with prompts, learning journal and referencing through sharing of learning performance and behavior significantly correlate with each other and learning achievement. In addition, the results revealed learning journal brings more effect on learning performance and achievement than self-assessment with prompts.