The board of directors of Consolidated Rail Corp. yesterday tapped veteran railroader L. Stanley Crane, former chairman and chief executive officer of the Southern Railway, to head the embattled organization next year.

Crane, who retired from Southern Oct. 1 in keeping with the company's mandatory retirement age of 65, will bring to the federally subsidized freight railroad nearly 43 years of experience with the very successful Southern and a reputation as an extremely able rail executive. Crane will succeed Edward G. Jordan, who is resigning after 4 1/2 years as Conrail's chief to become dean of the Graduate School of Business at Cornell University.

In commenting on Crane's election yesterday, Jordan, who served on the special search committee, said, "We wanted someone with experience as a chief executive, a successful railroad operating background and marketing experience. In Mr. Crane, Conrail has been able to secure the services of a person with these outstanding qualifications."

Crane will have his work cut out for him. There has been increasing criticism of Conrail on Capitol Hill, and its future will be debated vigorously next year. Conrail was formed on April 1, 1976, as a successor to bankrupt railroads in the Northeast and Midwest with $3.3 billion in federal funds earmarked to see it through to self-sufficiency. But this summer, Conrail told the government it will need at least another $1 billion -- and possibly $2 billion -- in federal investment beyond the already-authorized $3.3 billion.

Yesterday, Crane was optimistic, "As railroads move forward in a new era of regulatory reform, I believe that Conrail will have an opportunity to strengthen itself and, in doing so, become a part of a healthy railraod industry," he said in a statement. "I'm pleased that I will have the opportunity to play an active role and will do everything in my power to make Conrail a success."

At Southern, Crane worked in a number of supervisory positions in the mechanical, engineering and operating departments before being named executive vice president for operations in 1970. In 1976, he was named president and chief executive officer and became chairman and CEO in 1979.