Researchers will map the DNA of the bug responsible for the disease, Mycobacterium bovis, and analyse it using sophisticated mathematical and statistical models.
The scientists from the University of Glasgow hope to uncover vital information about the way TB is transmitted.
This is turn will help policy makers come up with more efficient strategies for curbing the spread of bovine TB.
Questions remain over the controversial culling of badgers, suspected of driving the epidemic.
The Government has announced that pilot badger culls in the UK will continue this year but will not now be rolled out to other areas.
An independent experts' report has found that "controlled shooting" of free-running badgers cannot deliver the level of culling needed to bring about a meaningful reduction of TB in cattle.
The new research will involve studying thousands of archived samples of bacteria that have been isolated from badgers and cattle over 20 years.
Lead scientist Professor Rowland Kao said: "This study is an excellent example of the potential for new technologies to transform our understanding of epidemiology.
"The mathematical models produced for this study are important for understanding not only the transmission of bovine TB, but also the dynamics of other infectious diseases."
The work, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), will be conducted over three years.