President Reagan yesterday nominated Philip F. Johnson, 42, a Chicago commodity lawyer, to be chairman of the Commodity Futures Trading Commission.

A partner in the Chicago law firm of Kirkland and Ellis, Johnson is one of the most prominent attorneys in the futures business and is the author of a two-volume book on commodity regulation that will be published later this year.

Johnson long has been reported to be in line for the post, but the oppointment had run into opposition from conservatives in the industry who feared he might take too active a stand as a regulator, and conservatives in government who questioned his political credentials.

Reagan's decision to name Johnson to head the CFTC is regarded as an effort to strengthen the commodity regulatory agency, which was largely ignored by the Carter administration.

Carter left office with one of the five commissioner's jobs vacant and another occupied by a holdover whose term had expired; the Republicans will be able to fill both posts and gain an immediate majority.

"Phil's appointment is the best thing that has ever happened to this agency; he brings a tremendous background in the industry," said Democratic Commissioner David Gartner, who frequently has feuded with the White House and outgoing CFTC Chairman James Stone, the most vigorous advocate of tightening commodity regulation, resigned as chairman after the election but remains a commission member.

The CFTC regulates trading in contracts for future delivery of commodities ranging from the traditional corn and soybeans to mortgages, government securities and precious metals.

Johnson has been counsel to the Chicago Board of Trade, the nation's biggest futures market and has been chairman of the American Bar Association's commodity section since it was created.

His close ties to the industry have been questioned by some Democrats in Congress. But recently liberals on the Hill have backed Johnson's nomination, contending his prestige as a commodity law specialist made him preferable to other candidates backed by farm groups and rural lawmakers.