Water-soluble CdSe nanocrystals were synthesized in a new alkali system at lower temperatures by using L-cysteine hydrochloride as a stabilizer and Na2SeSO3 as a selenium source to enable the synthesis of CdSe nanocrystals in a wider range of pH values. The CdSe nanocrystal powder was characterized by X-ray powder diffraction, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and transmission electron microscopy. We systematically investigated the effect of synthesis conditions on the optical properties of the L-cysteine hydrochloride-stabilized CdSe nanocrystals, and found that different sizes of CdSe nanocrystals can be obtained by changing the pH value, the molar ratio of L-cysteine hydrochloride to Cd2+, or the refluxing time. The emission maxima of the obtained CdSe nanocrystals can be tuned in a wider range from 477 to 575 nm by changing the pH value from 7 to 13. We observed an obvious blue-shift of the absorption and photoluminescence peak position by varying the molar ratio of L-Cys to Cd2+ from 3.5:1 to 2:1 at the same pH value. The size of the obtained nanocrystals increased and the full width at half maximum became narrower as reflux time increased. Transmission electron microscopy images indicate that the as-prepared CdSe nanocrystals have a good dispersion, which means that L-cysteine hydrochloride can control the grouping of CdSe nanocrystals excellently as a stabilizer in the new alkali system.