Miller was expected to stay with the charity for about a year.
Sir Paul Nurse, former Imperial Cancer Research Fund director, will stand in as interim chief executive until the charity finds a replacement.
It is possible that Professor Gordon McVie, director-general with responsibility for communications, might be offered the post. However, McVie is seriously ill with pneumonia and will not be back at work until next month.
According to Cancer Research, Miller left early because the first phase of the merger went so quickly. He was involved primarily in merging the IT and organisational systems of the two charities, and that stage is now largely completed, said the spokeswoman.