The invention discloses a green rapid-hardening early-strength magnesium phosphate-based healant and a preparation method thereof. The green rapid-hardening early-strength magnesium phosphate-based healant is composed of a material A and a material B; the material A is prepared via mixing of a phosphate, borax, a toughening ingredient, an accelerating component, a water retention ingredient, a water reducing ingredient, and a grinding aid dispersing agent; and the B material is prepared via mixing of magnesium oxide, flyash, silica fume, ground steel slag, chromium iron tailing slag powder, anhydrite, an expanding agent, and a grinding aid dispersing agent. According to the preparation method, industrial supplementary cementious materials (flyash, silica fume, and ground steel slag) are added into cement, so that cement fluidity and early strength are improved; industrial chromium iron tailing slag powder is added into the green rapid-hardening early-strength magnesium phosphate-based healant as a filling material, so that it is beneficial for cement hydration reaction, set cement compaction rate is increased, and at the same time heavy metal waste solidification is realized. The green rapid-hardening early-strength magnesium phosphate-based healant is capable of achieving balance between magnesium phosphate cement setting time and high early strength, and solving problems that shrinking percentage is large and bonding strength is low.