The high speed and high maneuvering stealth aircrafts severely compress the detection power of the radar seeker. It is one of the effective ways to solve this problem by increasing the time of phase-coherent accumulation to improve the sensitivity of the seeker. A long time phase-coherent accumulation algorithm based on instantaneous frequency measurement (IFM) is proposed to detect the stealth target for pulse Doppler radar seeker. This algorithm is applied to the target detection of radar seeker with the mature IFM technology in the field of electronic countermeasures. Through the blind estimation of the relative acceleration between missiles and targets and compensating the quadratic term in the echo signal, the spectrum broadening problem caused by the relative acceleration can be solved. After compensation, the accumulation time of the echo signal is increased, which improves the detection sensitivity of the seeker. By the simulation condition, this algorithm increases the intercept sensitivity of the seeker by 12.5 dB, which means the range is increased by more than one time. This algorithm can also be applied in the situation where higher order accelerated velocity exists.