Soldiers would probably get bigger percentage raises than federal secretaries and scientists under the president's new and complex plan to revamp the way the federal establishment compensates itself.

If approved by Congress the Carter plan would, by divorcing federal and military pay formulas, allow military personnel generally to get larger annual boosts than civil servants. In fact, if put into operation early next year, the proposal could raise military pay in October 1980 that would be from 3-to-5 percent more than that of civilian bureaucrats.

For government civilians, a major change would be to compare U.S. salary and fringe benefits against total compensation in industry and state and local government. Once that comparison was made, raises would be adjusted on an area-by-area basis.

Locally, the plan would link raises for 300,000 civilian government workers to salaries (and fringe benefits) for counterpart jobs here in private industry and state and local governments.

The 60,000 military personnel here, like their colleagues from Korea to Germany, would continue to get October adjustments based strictly on average percentage gains in industry. Fringes would not be compared in establishing military pay levels.

White House officials believe the new system would mean larger percentage raises for government employes in big cities and high-cost areas. On the other hand the area wage linkage would tend to give smaller increases to federal personnel in small towns.

Federal officials say that under the national rate system now used to divide federal pay among 18 grades, low-level government workers in big cities often are paid at or near the poverty level. On the other hand, they say, the same civil service jobs in small towns especially in the South and Southwest often put bureaucrafts among the local salary elite.

There were no suprises in the Carter pay plan, which was outlined to reporters as it was being officially delivered to Capitol Hill. Many parts of it stem from earlier task forces set up by the president, or incorporate ideas proposed in 1975 by a pay panel chaired by the late Vice President Nelson Rockefeller.

Officials say the new system will equalize government and industry pay, while it essentially will "neutralize" the impact federal payraises have on the private labor market.

Many officials believe that the present pay system, which is supposed to be a "catchup" with industry actually tends to unfairly stimulate bigger private sector boosts. The result, they say, is that it is both inflationary and also leaves federal and private workers squabbling that the other guy is overpaid.

Some effects if the president's pay plan:

Blue collar federal workers would lose some longevity pays steps that now give them, according to the White House, an 8 percent to 12 percent salary advantage over carpenters, drivers, mechanics and other craft workers in private industry.

Guaranteed pay differentials of from 25 percent to 7.5 percent, which now go to U.S. government workers in Alaska, Hawaii and Puerto Rico, would be dropped. Instead they would be linked to the going rate for similar local jobs.

The president still would retain the authority to trim or limit federal and military pay raises. Officals say the White House would be less likely to shave future boosts once the new system got into operation and was accepted by the public.

Nobody in government today would take a pay cut. But future raises for employes whom surveys find are "overpaid" compared to local industry would be smaller. By the same token, civil servants in Detroit, Boston, New York and other big cities would get larger percentage raises than under the present system, which is based on a national one-shot pay raise for all government employes.

Opposition to the Carter plan is expected from federal unions. Many view it, as a method to hold down government pay raises by statistically stretching the value of federal fringe benefits like retirement and leave in comparison with industry.