The precipitation behavior of secondary phase particles (SPPs) was investigated in Zr-1Nb-0.01Cu alloy prepared by various processing techniques. The results show that with the decrease of cold rolling and annealing steps, intermediate annealing temperatures, final annealing temperatures and time, the average sizes of SPPs decrease accordingly. The β-Zr phase formed at the intermediate annealing temperature (higher than 640 °C) is hard to dissolve in the matrix after final annealing treatment. During the long-time final annealing process, the SPPs with smaller size coalesce into larger particles by diffusion through the matrix gradually because of Ostwald ripening mechanism. It shows that the decrease of intermediate annealing temperature is more effective than other processing techniques for minimizing the size of SPPs. The average particle size smaller than 50 nm can be achieved by low intermediate/final annealing temperature (≤520 °C) or short annealing time (≤2 h) treatment. The investigations in the present paper are very meaningful to control the SPPs in Zr-Nb based alloys.