This comes after ex-president Wolfgang Niersbach resigned in November after claims he knew about and assisted in the making of payments to secure votes.
Niersbach denies the allegations.
A new president will be elected on 15 April with treasurer Reinhard Grindel favourite to take over.
Sandrock, who served as general secretary since 2012, said:  "It is good practice and normal to give a newly elected president of the DFB [German football federation] the chance to propose a new general secretary for election.
"For the good of our football and the DFB it is necessary to make a completely new start in a credible and consistent manner, also in terms of personnel."
In November, tax authorities raided the DFB's headquarters after it emerged the federation had made a secret payment of 6.7m euros (£4.6m) to Fifa in 2005. An internal audit failed to find any trace of the 6.7m euros in the DFB's tax documents. The DFB denies the claims.
German news weekly Der Spiegel had claimed the money had been used to set up a slush fund to buy votes in the 2006 World Cup bidding process.
Helmut Sandrock has resigned as German football federation general secretary, a week before the release of a report into alleged dubious payments to Fifa surrounding the 2006 World Cup bid.