[ $ulcorner$ ]Cost-Effectiveness Analysis$lrcorner$ has been wifely used to evaluate economic efficiency of R&D projects, but most of cost-effectiveness evaluation systems have some problems such as systematic method for setting and evaluating cost factors, estimation of single effect on each R&D project, and estimation of cross effects among R&D projects. To solve these problems, we have designed a new evaluation indicator called a $ulcorner$Cost-Cross Effect Integration Indicator$lrcorner$ including cross effects developed in this research. The major research findings are summarized as follows : (1) $ulcorner$Coist Estimation Model$lrcorner$, which estimates the cost factors divided into two classes of assembly product and system product and then integrates the total cost values, has been designed. (2) A new method for estimating parameters of cross effects among R&D projects has been developed. (3) $ulcorner$Cross Effects Estimation Model$lrcorner$ to estimate multi-effects and cross effects by completion time among several projects has been designed. (4) $ulcorner$Integration Estimation Indicator$lrcorner$ for setting priority on a project group has been extracted by combination of total cost value and total effect value.